Bioinformatics and ChipsBioinformatics and Chips

Bioinformatics is a very Bioinformatics is a very integral part of each step in integral part of each step in a chip project.a chip project.

Steps in a Chip ProjectSteps in a Chip Project

1 Biological question2 Design experiment3 Design chip4 Run experiment5 Read out chip6 Treat data7 Biological answer

First overview, then details

Biological QuestionBiological Question

A chip experiment is only worth doing, if it answers a question that is worth asking.

Design ExperimentDesign Experiment

Not every question can be answered with a chip experiment.

Some questions that can be answered with a chip experiment can also be answered with another (cheaper) experiment.

Design experimentDesign experiment

Probes on the chip:

UniqueReproducible

Run ExperimentRun Experiment

Like every binding study, chip experiments have a thermodynamic and a kinetic component.

Run ExperimentRun Experiment

Binding thermodynamics:

G = H - TSG = - R T ln(K)

G = 1.4 kCal/M ~ Factor 10 in K1 H-bond ~ 1 – 4 kCal/M

Chip Read Out is ‘Solved’Chip Read Out is ‘Solved’

And, what is more, it has nothing to do with bioinformatics.

Treat DataTreat Data

I assume this has been discussed in other sessions in this course.

Biological AnswerBiological Answer

This is not just bioinformatics.Everything you know can, and should, be used at this stage.

Knowledge neededKnowledge needed

No matter what chip-array software you use, you will want to know all there is to know about the genes/proteins that are on the chip. So, up-to-date databases are always needed.

Some toolsSome tools

BLASTSRSKEGG

www.cmbi.kun.nl

BLASTBLAST

BLASTBLAST

BLASTBLAST

BLASTBLAST

SRSSRS

SRSSRS

SRSSRS

SRSSRS

SRSSRS

KEGGKEGG

KEGGKEGG

KEGGKEGG

KEGGKEGG

KEGGKEGG

KEGGKEGG

SwissProtSwissProt

ID CRAM_CRAAB STANDARD; PRT; 46 AA.

AC P01542;

DT 21-JUL-1986 (Rel. 01, Created)

DT 21-JUL-1986 (Rel. 01, Last sequence update)

DT 01-NOV-1997 (Rel. 35, Last annotation update)

DE CRAMBIN.

GN THI2.

OS Crambe abyssinica (Abyssinian crambe).

OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;

OC euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons;

OC core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae;

OC Crambe.

SwissProtSwissProt

RN [1]RP SEQUENCE.RX MEDLINE; 82046542.RA TEETER M.M., MAZER J.A., L'ITALIEN J.J.;RT "Primary structure of the hydrophobic plant protein crambin.";RL Biochemistry 20:5437-5443(1981).

CC -!- FUNCTION: THE FUNCTION OF THIS HYDROPHOBIC PLANTCC SEED PROTEIN IS NOT KNOWN.CC -!- SIMILARITY: BELONGS TO THE PLANT THIONIN FAMILY.

DR PIR; A01805; KECX.DR PDB; 1CRN; 16-APR-87.DR PDB; 1CBN; 31-JAN-94.

SwissProtSwissProt

FT DISULFID 3 40FT DISULFID 4 32FT DISULFID 16 26FT VARIANT 22 22 P -> S.FT VARIANT 25 25 I -> L.FT STRAND 2 3FT HELIX 7 16FT TURN 17 19FT HELIX 23 30FT TURN 31 31FT STRAND 33 34FT TURN 42 43SQ SEQUENCE 46 AA; 4736 MW; F6ADE458 CRC32;>P1;CRAM_CRAAB

TTCCPSIVAR SNFNVCRLPG TPEAICATYT GCIIIPGATC PGDYAN*

SignificanceSignificance

PointersPointers

www. cmbi.kun.nl/www. cmbi.kun.nl/srs/www. cmbi.kun.nl/bioinf/tools/blast.shtmlwww. genome.ad.jp/kegg/www. affymetrix.com/www. dmd.nl/arrayNL/arrayNL.htmlwww. gene-chips.com/

(the blank in there is not real, but needed if you use this Windows thing)

PointersPointers

www. BioASP.nlBioinformatica.pagina.nljura.ebi.ac.uk:8765/gqsrv/submitSoon an CMBI/BioASP: Pedant

(the blank in there is not real, but needed if you use this Windows thing)