graph annotation: a tale of two binary relations

CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

Graph Annotation

Seattle/Bellevue Graphs – Data, Processing, Algorithms Meetup 5 August 2014

A Tale of Two Binary Relations

Benjamin J. Keller linkedin.com/in/bjkeller

Attribution-ShareAlike 3.0 Unported

http://linkedin.com/in/bjkeller

http://creativecommons.org/licenses/by-sa/3.0/

Context: Systems story telling

want to help user understand relationships in data so that they can construct stories about biological systems

How do we use biological information and data to go from a list of genes to a story about how symptoms of a genetic disease arise?

[ ]

Context: Systems Story Telling

Classification Reasoning

Model-based Reasoning

Narrative Reasoning

(based on B. Mirel, Supporting cognition in systems biology analysis; findings on users’ processes and design implications. Journal of Biomedical Discovery and Collaboration 2009; 4:1-17)

what of all this is the right

stuff?

how does it fit together?

how does it do something?

what stories does it tell?

http://www.j-biomed-discovery.com/content/4/1/2/abstract

Context: Systems Story Telling

Classification Reasoning

Model-based Reasoning

Narrative Reasoning

individual components

networks/graphs of

components

system fragments

“whole” systems

roles

contextual classes

Grouping

PatternsComposition

Two kinds of binary relations

individual components

networks/graphs of

components

roles

contextual classes

Two kinds of binary relations

component

component

annotation

component

Incidence relation

Graph

,( )

,( )

Grouping

Start with - a network graph of genes, and - contextual annotations for each

Want to visualize what goes together

[ saw this before in cytoscape.js presentation ]

Grouping (hypergraph visualization)

MeSH: Calcium

GO BP: Metal Ion TransportGO MF: Gated Channel ActivityGO MF: Cation Channel Activity

GO MF: Voltage-Gated Ion Channel Activity

MeSH: Phosphorylation

MeSH: Signal Transduction

MeSH: Intercellular Signaling Peptides and Proteins

MeSH: Rats

MeSH: Nerve Tissue Proteins

MeSH Ion Channel Gating

CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

Simplified GroupingsMeSH: Calcium






CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium




MeSH: Rats


CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium





CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium



MeSH: Rats


CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium






CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium




MeSH: Rats


CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium





CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium



MeSH: Rats


CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

computed with BLOSOM (Zhao L, Zaki MJ, Ramakrishnan N., KDD 2006, 827-832), support=5

Human-edited Groupings

MeSH: Calcium

GO BP: Metal Ion TransportGO MF: Gated Channel ActivityGO MF: Cation Channel ActivityORMeSH Ion Channel Gating




CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1

KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

MeSH: Calcium

GO BP: Metal Ion TransportGO MF: Gated Channel ActivityGO MF: Cation Channel ActivityORMeSH Ion Channel Gating



CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1

KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

“user” merged/deleted annotations

Formal Concept Analysis

CACNA1C

Ion transport protein

KCNC1

KCNC2

RYR2

SCN2A

Beta1 adrenergic receptor signaling pathway

CACNB3

GNB1

PRKACA


cation transport

CACNA2D4

SCN1B

SCNN1B

metal ion transport

channel activity

ion channel activity

gated channel activity

cation channel activity

alkali metal ion binding

calcium channel activity

voltage-gated channel activity

transmembrane transporter activity

voltage-gated ion channel activity

substrate specific channel activity

voltage-gated cation channel activity

ion transmembrane transporter activity

substrate-specific transporter activity

cation transmembrane transporter activity

passive transmembrane transporter activity

metal ion transmembrane transporter activity

substrate-specific transmembrane transporter activity

ANK3

RatsCNTN1

PIK3R1

Animals

SMAD2

SMAD3

CABP1

Calcium

SRI

Ankyrins

SPTBN4

CRKL

Cell Line

FADD

Myocardium

Jurkat CellsFAS

PPM1A Smad2 Protein

Phosphorylation

Ranvier's Nodes

Sodium Channels

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction

Nerve Tissue ProteinsRIMS1

Patch-Clamp Techniques

Sodium Channel Blockers

Calcium Channels, L-Type

Two-Hybrid System Techniques

Ryanodine Receptor Calcium Release Channel

Intracellular Signaling Peptides and Proteins

• Algebraic approach to studying data as incidence relation b/w objects and attributes

• Construct formal concepts (biclusters)

• Relate to form formal concept lattice

Formal Concept

CACNA1C


KCNC1

KCNC2

RYR2

SCN2A


CACNB3

GNB1

PRKACA


cation transport

CACNA2D4

SCN1B

SCNN1B

metal ion transport

channel activity




alkali metal ion binding


voltage-gated channel activity


voltage-gated ion channel activity


voltage-gated cation channel activity







ANK3

RatsCNTN1

PIK3R1

Animals

SMAD2

SMAD3

CABP1

Calcium

SRI

Ankyrins

SPTBN4

CRKL

Cell Line

FADD

Myocardium

Jurkat CellsFAS

PPM1A Smad2 Protein

Phosphorylation

Ranvier's Nodes

Sodium Channels

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction

Nerve Tissue ProteinsRIMS1

Patch-Clamp Techniques

Sodium Channel Blockers

Calcium Channels, L-Type




• Can view incidence relation as bipartite graph

• A formal concept is a biclique: a pair of vertices (A,B) such that for each object a in A there is an edge (a,b) for every attribute b in B

• Can construct as closure

Ex: Signal Transduction


GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction





GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction




Subconcept


GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction





GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction




Subconcept relationship


GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction





GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction




more objects/fewer attributes

fewer objects/more attributes

Subconcept relationship


GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction





GNB1

PRKACA


Rats

PIK3R1

Animals

SMAD2

SMAD3

Calcium

CRKL

Cell Line

FADD

Myocardium

Jurkat Cells

FAS

PPM1A

Smad2 Protein

Phosphorylation

Calcium Channels

Precipitin Tests

Protein Subunits

Ion Channel Gating

Signal Transduction




CRKL, FADD, FAS, GNB1, PIK3R1, PPM1A, PRKACA, SMAD2, SMAD3; 744175

FADD, FAS, PIK3R1, SMAD2, SMAD3; 744175,

748642

Concept Lattice

ANK3, CABP1, CACNA1C, CACNA2D4, CACNB3, CNTN1, CRKL, FADD, FAS, GNB1, KCNC1,

KCNC2, PIK3R1, PPM1A, PRKACA, RIMS1, RYR2, SCN1B, SCN2A, SCNN1B, SMAD2, SMAD3,

SPTBN4, SRI;

CACNA1C, CACNB3, GNB1, PRKACA, RYR2; 617414,

617437

CACNA1C, CACNA2D4, CACNB3, KCNC1, KCNC2, RYR2, SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360,

737390, 737431, 737548

ANK3, CACNA1C, CNTN1, GNB1, PIK3R1, PRKACA,

SCNN1B; 737748

CNTN1, GNB1, PIK3R1, PRKACA, SMAD2, SMAD3;

738083

CABP1, CACNA1C, PRKACA, RYR2, SRI; 738118

ANK3, SCN1B, SPTBN4; 738391

ANK3, SCNN1B, SPTBN4; 742325

CABP1, CACNA1C, CACNB3, PRKACA, RYR2; 742512

CACNA1C, GNB1, PIK3R1, PRKACA, SCN1B, SCN2A,

SCNN1B; 742806

ANK3, CACNA1C, CACNB3, GNB1, SCN1B, SCN2A,

SCNN1B; 743584


CNTN1, RIMS1, SCN1B, SCN2A, SPTBN4; 744929

CABP1, CACNA1C, CACNB3, SCN1B, SCN2A, SCNN1B;

745316

CNTN1, SCN2A, SCNN1B; 745760

CABP1, CACNA1C, CACNA2D4, CACNB3;

745845

CACNA1C, CACNA2D4, CACNB3; 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

745845

CABP1, CACNA1C, CACNB3; 742512, 745316, 745845

CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760

CACNA1C, CACNB3, SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 743584,

745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760

GNB1, PIK3R1, PRKACA, SMAD2, SMAD3; 738083,

744175

CRKL, FADD, PIK3R1, PRKACA, SMAD2, SMAD3; 738855, 744175

CRKL, FADD, FAS, PIK3R1; 740606,

744175

CRKL, PIK3R1, PPM1A, PRKACA, SMAD2, SMAD3; 742292, 744175

FADD, GNB1, PIK3R1, SMAD2, SMAD3; 744175,

747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642

FADD, PIK3R1, SMAD2, SMAD3; 738855, 744175, 747193, 748642

GNB1, PIK3R1, SMAD2, SMAD3; 738083, 744175,

747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584

ANK3, CACNA1C, GNB1, SCNN1B; 737748, 743584

ANK3, SCN1B, SCN2A, SCNN1B; 742390, 743584

CACNA1C, GNB1, SCN1B, SCN2A, SCNN1B; 742806,

743584

CACNA1C, GNB1, PIK3R1, PRKACA, SCNN1B; 737748,

742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584

CACNA1C, SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742806, 743584,

745316

CACNA1C, CACNB3, PRKACA, RYR2; 617414,

617437, 742512

CABP1, CACNA1C, PRKACA, RYR2; 738118, 742512

CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325

CRKL, PIK3R1, PRKACA, SMAD2, SMAD3; 738855, 742292, 744175

PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175

PIK3R1, PRKACA, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175

PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642

CACNA1C, PRKACA, RYR2, SRI; 738118, 739640, 748541

CACNA1C, PRKACA, RYR2; 617414, 617437, 738118, 739640, 742512, 748541

CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541

CNTN1, GNB1, PIK3R1, PRKACA;

737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760

CACNA1C, GNB1, PRKACA; 617414, 617437, 737748,

742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541

CACNA1C, KCNC1, KCNC2, RYR2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255,

737304, 737332, 737360, 737390, 737431, 737548

KCNC1, KCNC2, SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255,

737304, 737332, 737360, 737390, 737431, 737548

CACNA1C, CACNA2D4, CACNB3, RYR2; 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548

CACNA1C, CACNA2D4, CACNB3, KCNC1, KCNC2, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737304, 737332, 737360,

737390, 737431, 737548

CACNA1C, CACNB3, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, KCNC1, KCNC2, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360,

737390, 737431, 737548

CACNA1C, KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548

KCNC1, KCNC2, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

Top



SPTBN4, SRI;


617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584




745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

formally: concept formed by closure of empty set of attributes alternative: concept with attributes shared by all objects

Bottom

formally: concept formed by closure of empty set of objects alternative: concept with objects with all attributes



SPTBN4, SRI;


617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584




745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

Co-atoms



SPTBN4, SRI;


617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584CRKL, FADD, FAS, GNB1, PIK3R1, PPM1A, PRKACA, SMAD2, SMAD3; 744175



745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

immediate subconcepts of the top concept

ChainANK3, CABP1, CACNA1C, CACNA2D4, CACNB3,

CNTN1, CRKL, FADD, FAS, GNB1, KCNC1, KCNC2, PIK3R1, PPM1A, PRKACA, RIMS1, RYR2,

SCN1B, SCN2A, SCNN1B, SMAD2, SMAD3, SPTBN4, SRI;


617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584




745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

Anti-chain



SPTBN4, SRI;


617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584




745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

Groupings (again)

• A simplified grouping is represented by a minimal anti-chain in the concept lattice that best covers objects (e.g., vertices)

• Heuristic: a. generate concepts for individual annotations b. for each, create chain by selecting subconcept with

most objects c. select from chains such that vertex set is covered

Ex: Grouping (BLOSOM)



SPTBN4, SRI;


617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584




745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

Ex: Grouping (BLOSOM)ANK3, CABP1, CACNA1C, CACNA2D4, CACNB3,




617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584




745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

MeSH: Calcium





CRKL

ANK3

CABP1

CACNA2D4

CACNB3

GNB1

PCBD1

RIMS1

PPM1A

PRKACA

RYR2

SRI

CACNA1C

FASFADD

CNTN1

HOOK1

KCNC1 KCNC2

SMAD3

SMAD2

PIK3R1

SPTBN4

SCN1B

SCNN1B

SCN2A

note: BLOSOM finds minimal generator for a concept: smallest set of attributes with concept as closure

Graph edges and grouping

RYR2CACNA1C

In what situations does this interaction occur?

Graph edges

RYR2CACNA1C

CACNA1C


RYR2



cation transport

metal ion transport

channel activity













Myocardium

Calcium Channels

Graph edges

CACNA1C


RYR2



cation transport

metal ion transport

channel activity













Myocardium

Calcium Channels

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

FilterANK3, CABP1, CACNA1C, CACNA2D4, CACNB3,




617437


737390, 737431, 737548


SCNN1B; 737748


738083






SCNN1B; 742806


SCNN1B; 743584




745316



745845


745845


CNTN1, SCNN1B; 737748, 745760

CNTN1, SCN2A; 744929, 745760

SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584, 745316,

745760


745316

SCN1B, SPTBN4; 738391, 744929

SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316

CNTN1; 737748, 738083, 744929,

745760

SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 742390,

742806, 743584, 744929, 745316, 745760


744175



744175



747193


748642

FADD, FAS, PIK3R1; 740606, 744175, 748642



747193

CACNA1C, CACNB3, GNB1; 617414, 617437, 743584




743584


742806

CACNA1C, GNB1, SCNN1B; 737748, 742806, 743584


745316


617437, 742512


CABP1, CACNA1C; 738118, 742512, 745316, 745845

CACNA1C, CACNB3; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390,

737431, 737548, 742512, 743584, 745316, 745845

ANK3, SCN1B; 738391, 742390, 743584

ANK3, SCNN1B; 737748, 742325, 742390, 743584

SCN1B, SCN2A, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 742390, 742806, 743584,

745316

ANK3, SPTBN4; 738391, 742325


PPM1A, SMAD2, SMAD3; 741302, 742292, 744175

SMAD2, SMAD3; 738083, 738855, 741302, 742292, 742793, 744175, 747193,

748642

CRKL, FADD, PIK3R1; 738855, 740606, 744175

FADD, PIK3R1; 738855, 740606, 744175, 747193,

748642

PIK3R1, SMAD2, SMAD3; 738083, 738855, 742292, 742793, 744175, 747193,

748642

CRKL, PIK3R1; 738855, 740606, 742292, 744175


PIK3R1; 737748, 738083, 738855, 740606, 742292, 742793, 742806, 744175,

747193, 748642

SPTBN4; 738391, 742325, 744929

SCN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 738391, 742390,

742806, 743584, 744929, 745316

ANK3; 737748, 738391, 742325, 742390, 743584

; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738083, 738118, 738391, 738855, 739640, 740606, 741302, 742292, 742325, 742390, 742512, 742793, 742806, 743584, 744175, 744929, 745316, 745760,

745845, 747193, 748541, 748642



CACNA1C; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 738118, 739640, 742512, 742806,

743584, 745316, 745845, 748541


737748, 738083

GNB1, PIK3R1, PRKACA; 737748, 738083, 742806,

744175

GNB1, PIK3R1; 737748, 738083, 742806, 744175,

747193

PIK3R1, PRKACA; 737748, 738083, 738855, 742292, 742793, 742806, 744175

SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742325, 742390, 742806, 743584,

745316, 745760


742806

CACNA1C, GNB1; 617414, 617437, 737748, 742806,

743584

CACNA1C, SCNN1B; 733740, 733911, 736632, 736738, 736786, 736810, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 737748, 742806, 743584, 745316

GNB1, PRKACA; 617414, 617437, 737748, 738083,

742806, 744175

GNB1; 617414, 617437, 737748, 738083, 742806, 743584, 744175, 747193

PRKACA; 617414, 617437, 737748, 738083, 738118, 738855, 739640, 742292, 742512, 742793, 742806, 744175, 748541


737304, 737332, 737360, 737390, 737431, 737548


737304, 737332, 737360, 737390, 737431, 737548



737390, 737431, 737548


737548, 743584, 745316

CACNA1C, SCN1B, SCN2A; 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316


737390, 737431, 737548


737431, 737548


737548

CACNA1C, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431, 737548,

742806, 743584, 745316

CACNA1C, CACNB3, RYR2; 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548,

742512

KCNC1, KCNC2, SCN2A; 614163, 733740, 733911, 736632, 736738, 736786, 736810, 736836, 737094, 737232, 737234, 737255, 737293, 737304, 737332, 737360, 737390, 737431,

737548

CACNA1C, RYR2; 614163, 617414, 617437, 733740, 733911, 736632, 736738, 736786, 736810, 736839, 737232, 737255, 737304, 737332, 737360, 737390, 737431, 737548, 738118, 739640, 742512,

748541

CACNA1C, PRKACA; 617414, 617437, 737748, 738118, 739640, 742512,

742806, 748541

Patterns

• Previous examples project annotations onto the graph

• For patterns, project the graph onto the annotations

• Can use lattice to find emergent schema (Banks et al.)

• One heuristic: for each edge (a1,a2) find concepts for a1 and a2, and follow pair of chains upward, adding edges for new objects, until cannot add more

Banks E, Nabieva E, Chazelle B, Singh M (2008) PLoS Comput Biol 4(10): e1000203

Constructing Schema

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Schema: Moving up chains

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Schema: moving up chains

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Extracting Schema

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Final Schema

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�Recurrent pattern in graph – could be used to match other graphs

More…

• Could keep going …

• Possible to extract association rules, decision trees and more from concept lattice and use these to annotate functional relationships in graphs (which again is something that has been done other ways)

• Also possible to work with multi-valued incidence relations (e.g., numeric data)

Inspired and informed by working with Barbara Mirel and NCIBI DBP scientists at U.Michigan

Resources

B Ganter, R Wille. Formal Concept Analysis: Mathematical Foundations, Springer-Verlag, 1999. !F Kriegel, Visualization of Conceptual Data with Methods of Formal Concept Analysis. Thesis, Technische Universität Dresden, 2012. !http://www.upriss.org.uk/fca/fca.html

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CCMQFjAA&url=http%3A%2F%2Flat.inf.tu-dresden.de%2F~francesco%2Ftudresden%2Fdoc%2Fdiploma-thesis.pdf&ei=q2riU_-iEYjtoASOkYGABg&usg=AFQjCNFgFCOYU-PWJJxTvgUIV8Vzq9UzWA&bvm=bv.72197243,d.cGU

http://www.upriss.org.uk/fca/fca.html

graph annotation: a tale of two binary relations

Data & Analytics

mesh ion channel gating

phosphorylation mesh

rats mesh

cation channel activity

signal transduction

gated channel activity

simplied groupings mesh

hypergraph visualization