gene association networks - large-scale integration of data and text
TRANSCRIPT
![Page 1: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/1.jpg)
Gene association networks
Large-scale integration of data and text
Lars Juhl Jensen
![Page 2: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/2.jpg)
9.6 million genes
![Page 3: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/3.jpg)
association network
![Page 4: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/4.jpg)
guilt by association
![Page 5: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/5.jpg)
![Page 6: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/6.jpg)
genomic context
![Page 7: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/7.jpg)
gene fusion
![Page 8: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/8.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 9: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/9.jpg)
phylogenetic profiles
![Page 10: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/10.jpg)
Korbel et al., Nature Biotechnology, 2004
![Page 11: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/11.jpg)
experimental data
![Page 12: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/12.jpg)
gene coexpression
![Page 13: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/13.jpg)
![Page 14: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/14.jpg)
physical interactions
![Page 15: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/15.jpg)
Jensen & Bork, Science, 2008
![Page 16: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/16.jpg)
curated knowledge
![Page 17: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/17.jpg)
protein complexes
![Page 18: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/18.jpg)
![Page 19: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/19.jpg)
pathways
![Page 20: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/20.jpg)
Letunic & Bork, Trends in Biochemical Sciences, 2008
![Page 21: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/21.jpg)
many databases
![Page 22: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/22.jpg)
different formats
![Page 23: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/23.jpg)
different identifiers
![Page 24: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/24.jpg)
variable quality
![Page 25: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/25.jpg)
not comparable
![Page 26: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/26.jpg)
hard work
![Page 27: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/27.jpg)
(Ph.D. students)
![Page 28: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/28.jpg)
parsers
![Page 29: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/29.jpg)
mapping files
![Page 30: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/30.jpg)
quality scores
![Page 31: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/31.jpg)
affinity purification
![Page 32: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/32.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 33: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/33.jpg)
score calibration
![Page 34: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/34.jpg)
gold standard
![Page 35: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/35.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 36: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/36.jpg)
implicit weighting by quality
![Page 37: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/37.jpg)
common scale
![Page 38: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/38.jpg)
cross-species transfer
![Page 39: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/39.jpg)
Franceschini et al., Nucleic Acids Research, 2013
![Page 40: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/40.jpg)
missing most of the data
![Page 41: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/41.jpg)
>10 km
![Page 42: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/42.jpg)
too much to read
![Page 43: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/43.jpg)
text mining
![Page 44: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/44.jpg)
comprehensive lexicon
![Page 45: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/45.jpg)
cyclin dependent kinase 1
![Page 46: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/46.jpg)
CDC2
![Page 47: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/47.jpg)
orthographic variation
![Page 48: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/48.jpg)
spaces and hyphens
![Page 49: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/49.jpg)
cyclin dependent kinase 1
![Page 50: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/50.jpg)
cyclin-dependent kinase 1
![Page 51: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/51.jpg)
prefixes and suffixes
![Page 52: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/52.jpg)
CDC2
![Page 53: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/53.jpg)
hCdc2
![Page 54: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/54.jpg)
“black list”
![Page 55: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/55.jpg)
SDS
![Page 56: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/56.jpg)
co-mentioning
![Page 57: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/57.jpg)
counting
![Page 58: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/58.jpg)
within documents
![Page 59: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/59.jpg)
within paragraphs
![Page 60: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/60.jpg)
within sentences
![Page 61: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/61.jpg)
quality scores
![Page 62: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/62.jpg)
score calibration
![Page 63: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/63.jpg)
cross-species transfer
![Page 64: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/64.jpg)
combine all evidence
![Page 65: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/65.jpg)
Szklarczyk et al., Nucleic Acids Research, 2015string-db.org
![Page 66: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/66.jpg)
web resource
![Page 67: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/67.jpg)
download files
![Page 68: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/68.jpg)
REST API
![Page 69: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/69.jpg)
Bioconductor package
![Page 70: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/70.jpg)
Cytoscape App
![Page 71: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/71.jpg)
AcknowledgmentsDamian Szklarczyk
Michael KuhnAndrea Franceschini
Milan SimonovicAlexander Roth
Sune Pletscher-FrankildJohn “Scooter” MorrisChristian von Mering
Peer Bork
![Page 72: Gene association networks - Large-scale integration of data and text](https://reader036.vdocuments.site/reader036/viewer/2022070513/5884b0bb1a28ab76798b6a99/html5/thumbnails/72.jpg)
Unacknowledgments
Do yourself a favor, don’t fly