The STRING database - Quality scores for heterogeneous interaction data
-
Upload
lars-juhl-jensen -
Category
Technology
-
view
1.231 -
download
0
description
Transcript of The STRING database - Quality scores for heterogeneous interaction data
![Page 1: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/1.jpg)
The STRING databaseQuality scores for heterogeneous interaction data
Lars Juhl Jensen
EMBL Heidelberg
![Page 2: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/2.jpg)
data integration
![Page 3: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/3.jpg)
Jensen et al., Drug Discovery Today: Targets, 2004
![Page 4: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/4.jpg)
functional interactions
![Page 5: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/5.jpg)
Genomic neighborhood
Species co-occurrence
Gene fusions
Database imports
Experimental interaction data
Microarray expression data
Literature mining
![Page 6: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/6.jpg)
373 proteomes
![Page 7: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/7.jpg)
model organism databases
![Page 8: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/8.jpg)
Ensembl
![Page 9: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/9.jpg)
Genome Reviews
![Page 10: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/10.jpg)
RefSeq
![Page 11: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/11.jpg)
genomic context methods
![Page 12: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/12.jpg)
gene fusion
![Page 13: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/13.jpg)
![Page 14: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/14.jpg)
gene neighborhood
![Page 15: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/15.jpg)
![Page 16: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/16.jpg)
phylogenetic profiles
![Page 17: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/17.jpg)
![Page 18: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/18.jpg)
scoring schemes
![Page 19: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/19.jpg)
benchmarking
![Page 20: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/20.jpg)
cross-species transfer
![Page 21: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/21.jpg)
primary experimental data
![Page 22: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/22.jpg)
many sources
![Page 23: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/23.jpg)
different formats
![Page 24: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/24.jpg)
different gene identifiers
![Page 25: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/25.jpg)
redundancy
![Page 26: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/26.jpg)
physical protein interactions
![Page 27: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/27.jpg)
IntAct
![Page 28: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/28.jpg)
BINDBiomolecular Interaction Network Database
![Page 29: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/29.jpg)
MINTMolecular Interactions Database
![Page 30: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/30.jpg)
DIPDatabase of Interacting Proteins
![Page 31: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/31.jpg)
GRIDGeneral Repository for Interaction Datasets
![Page 32: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/32.jpg)
HPRDHuman Protein Reference Database
![Page 33: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/33.jpg)
PSI-MI
![Page 34: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/34.jpg)
reference proteomes
![Page 35: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/35.jpg)
merge data by publication
![Page 36: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/36.jpg)
thousands of interactions
![Page 37: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/37.jpg)
correct interactions
![Page 38: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/38.jpg)
wrong interactions
![Page 39: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/39.jpg)
scoring scheme
![Page 40: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/40.jpg)
complex pull-down
![Page 41: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/41.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 42: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/42.jpg)
log[(N12·N)/((N1+1)·(N2+1))]
![Page 43: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/43.jpg)
yeast two-hybrid
![Page 44: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/44.jpg)
non-shared interactors
![Page 45: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/45.jpg)
-log((N1+1)·(N2+1))
![Page 46: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/46.jpg)
not directly comparable
![Page 47: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/47.jpg)
calibrate vs. gold standard
![Page 48: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/48.jpg)
![Page 49: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/49.jpg)
other types of evidence
![Page 50: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/50.jpg)
co-expression
![Page 51: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/51.jpg)
GEOGene Expression Omnibus
![Page 52: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/52.jpg)
species-specific datasets
![Page 53: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/53.jpg)
correlation coefficient
![Page 54: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/54.jpg)
calibrate vs. gold standard
![Page 55: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/55.jpg)
directly comparable
![Page 56: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/56.jpg)
curated knowledge
![Page 57: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/57.jpg)
many sources
![Page 58: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/58.jpg)
different formats
![Page 59: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/59.jpg)
different gene identifiers
![Page 60: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/60.jpg)
redundancy
![Page 61: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/61.jpg)
protein complexes
![Page 62: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/62.jpg)
MIPSMunich Information center
for Protein Sequences
![Page 63: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/63.jpg)
Gene Ontology
![Page 64: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/64.jpg)
pathway databases
![Page 65: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/65.jpg)
KEGGKyoto Encyclopedia of Genes and Genomes
![Page 66: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/66.jpg)
Reactome
![Page 67: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/67.jpg)
PIDNCI-Nature Pathway Interaction Database
![Page 68: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/68.jpg)
STKESignal Transduction Knowledge Environment
![Page 69: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/69.jpg)
BioPAX
![Page 70: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/70.jpg)
reference proteomes
![Page 71: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/71.jpg)
literature mining
![Page 72: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/72.jpg)
MEDLINE
![Page 73: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/73.jpg)
SGDSaccharomyces Genome Database
![Page 74: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/74.jpg)
The Interactive Fly
![Page 75: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/75.jpg)
OMIMOnline Mendelian Inheritance in Man
![Page 76: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/76.jpg)
different gene identifiers
![Page 77: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/77.jpg)
synonyms lists
![Page 78: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/78.jpg)
black list
![Page 79: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/79.jpg)
flexible matching
![Page 80: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/80.jpg)
co-occurrence
![Page 81: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/81.jpg)
log[(N12·N)/((N1+1)·(N2+1))]
![Page 82: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/82.jpg)
NLPNatural Language Processing
![Page 83: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/83.jpg)
Gene and protein namesCue words for entity recognitionVerbs for relation extraction
[nxgene The GAL4 gene]
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
![Page 84: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/84.jpg)
calibrate vs. gold standard
![Page 85: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/85.jpg)
directly comparable
![Page 86: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/86.jpg)
combine all evidence
![Page 87: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/87.jpg)
spread over many species
![Page 88: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/88.jpg)
transfer by orthology
![Page 89: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/89.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 90: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/90.jpg)
two modes
![Page 91: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/91.jpg)
![Page 92: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/92.jpg)
orthologous groups
![Page 93: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/93.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 94: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/94.jpg)
![Page 95: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/95.jpg)
fuzzy orthology
![Page 96: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/96.jpg)
von Mering et al., Nucleic Acids Research, 2005
![Page 97: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/97.jpg)
add probabilistic scores
![Page 98: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/98.jpg)
P = 1-(1-P1).(1-P2).(1-P3)…
![Page 99: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/99.jpg)
Genomic neighborhood
Species co-occurrence
Gene fusions
Database imports
Experimental interaction data
Microarray expression data
Literature mining
![Page 100: The STRING database - Quality scores for heterogeneous interaction data](https://reader033.fdocuments.in/reader033/viewer/2022052622/558e70e91a28ab66638b468d/html5/thumbnails/100.jpg)
Acknowledgments
The STRING team– Christian von Mering
– Michael Kuhn
– Berend Snel
– Martijn Huynen
– Sean Hooper
– Samuel Chaffron
– Julien Lagarde
– Mathilde Foglierini
– Peer Bork
Literature mining project– Jasmin Saric
– Rossitza Ouzounova
– Isabel Rojas