[EcoliNet: a network by integration of all data-type-specific networks (CC, CX, DC, GN, HT, LC, PG)]
Integrated network#genes#links
EcoliNet v.14099 genes95520 links

[Positive goldstandard co-functional gene pairs]
Positive goldstandard co-functional gene pairs#genes#links
Co-functional gene pairs by GO-BP or EcoCyc annotations1835 genes10804 links
Co-functional gene pairs by GO-BP annotations1474 genes6896 links
Co-functional gene pairs by EcoCyc annotations885 genes4694 links

[Integrated networks for each of data types]
Data type#linksDescription
CC50528Inferred links by co-citation of two genes across 57,062 PubMed Central articles for E. coli biology (based on high-dimensional gene expression data)
CX67494Inferred links by co-expression pattern of two genes (based on high-dimensional gene expression data)
DC9643Inferred links by co-occurrence of protein domains between two coding genes
GN23439Inferred links by similar genomic context of bacterial orthologs of two E. coli genes
HT15543Inferred Links by high-throughput protein-protein interactions
LC1073Inferred Links by small/medium-scale protein-protein interactions (collected from protein-protein interaction data bases)
PG17504Inferred links by similar phylogenetic profiles between two E. coli genes

[CX networks based on individual expression data sets (GEO series)]
DB/data setReference (PMID)Edge list download#linkExperiment description
GSE711027315download36200Tryptophan metabolism response in E. coli
GSE110615129285download30071aerobic knock-out
GSE110718828895download26500anaerobic knock-out
GSE173015535862download5096mRNA abundance from wild type
GSE178015817786download8892The expression profile of Escherichia coli K-12 in response to minimal, optimal and excess copper concentrations
GSE2999NAdownload27495Cisplatin-induced gene expression in DNA adenine methyltransferase (dam) and mismatch repair deficient E. coli
GSE325016141204download12037BW25113 glucose to acetate transition
GSE359117921306download8972A reassesment of the FNR regulon and the effects of nitrate,nitrite, narXL and narQP
GSE390517222132download7002Temporal Biofilm Expression of E. coli K-12 after 4, 7, 15, and 24 hr
GSE397714981237download19197Comparative Transcript Abundance in E. Coli Degradosome Mutants and their Parental Strains
GSE436316626502download19004Recovery from stationary phase in LB + 0.2 % glucose
GSE440817009874download11070Transcriptional consequences of DNA gyrase inhibition
GSE451115601715download12005pH Regulates Genes for Flagellar Motility, Catabolism, and Oxidative Stress in Escherichia coli K-12
GSE603320863252download15203Reference Design time-course
GSE683617214507download14450Large-Scale Mapping and Validation of E. coli Transcriptional Regulation from a Compendium of Expression Profiles
GSE732619304752download5241Expression profiles during cell death programmed by a restriction-modification system in E. coli
GSE739817768236download12927Expression data from E. coli covering four phases of growth in Fis KO and WT (Fis+) strains
GSE7477NAdownload19717 Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
GSE757317494765download13948Identification of NO Response Network in E. coli
GSE788517979199download25060Gene expression of E. coli MG1655 wild type and rpoS knock-out strains
GSE992318528414download17890Indole cell signaling occurs primarily at low temperatures in Escherichia coli
GSE1015818192383download7079Expression of Escherichia coli treated with cefsulodin and mecillinam, alone and in combination
GSE1085518467556download23988MG1655 temperature O2 response normalized data Tavazoie
GSE1104119767843download19800Overlapping and unique responses of E. coli to adverse conditions
GSE1108718430135download10970E. coli Isoleucine starvation and stringent response network
GSE1118319194530download13890Identification of the Escherichia coli HU regulon
GSE1279718843507download13907Control of RpoS in global gene expression of Escherichia coli in minimal media
GSE1287719091747download12032Transcriptional profiling of Escherichia coli after addition of CO-RMs to aerobically growing cells
GSE1304819091747download18914Transcriptional profiling of Escherichia coli
GSE1341819376922download30611Gene expression of E. coli MG1655 at attachment, colony formation and maturation during biofilm formation
GSE1344419536200download38923Identification of isobutanol response network of E. coli
GSE1366619798444download24763Evolution of E. coli transcriptome under osmotic-stress with and without RpoS
GSE1540520008510download90421Expression data from E. coli cells overexpressing GraL for long periods of time
GSE1540620008510download41684Expression data from E. coli cells overexpressing GraL for short and long periods of time
GSE1540919366454download14828Amino acid/Nucleotide perturbation in Escherichia coli
GSE1550021057108download10003Analysis of differences in gene expression due to small adaptive mutations in RNA polymerase B' subunit (rpoC)
GSE1697320118358download3492Functional Genomic Study of Exogenous n-Butanol Stress in Escherichia coli
GSE1727619893610download39945Transcriptional profiling of an evolved polymorphism in E. coli
GSE1758419703305download12225Transcriptional effects of CRP* expression in Escherichia coli
GSE1974220478253download13966Expression profiling of E.coli K-12 wild-type vs. delta dksA cells upon amino acid starvation
GSE2030520461071download31877Time resolved response of E. coli to 5 different stress conditions
GSE2183920709841download16926Transcriptome analysis of wild type E. coli (K-12 MG1655) comparing to mutant E. coli strain (ECOM4) under aerobic and anaerobic conditions
GSE2186921785135download15320Expression profiles of evolved clones isolated at various stages during adaptive experimental evolution of E. coli
GSE2618722016571download13001Transcriptional profiling of Escherichia coli during a transition from zinc starvation to surfeit
GSE2841222018139download7004Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon beta in high cell density fed batch cultures using time course transcriptomic data
GSE2879522056927download9926Expression data from E. coli cells overexpressing either GreA or GreB in ppGpp0 cells in the dksA+ or dksA- background
GSE2942421948837download5921Functional genomics study of endogenous free fatty acid overproduction in Escherichia coli
GSE3063922645336download8910Evolution of gene expression during long term coexistence in a bacterial evolution experiment
GSE3133316249312download29958NIA Neuroarray dehydration
GSE3256122038610download18815Investigating the impact of heterologous expression of the Micrococcus luteus FabH on global transcription in Escherichia coli
GSE3256222122981download13089Trimethoprim response in Escherichia coli in bacteriostatic and bactericidal conditions
GSE3314716204189download32077Expression data from laboratory evolution of Escherichia coli on lactate or glycerol
GSE3402322295907download21682Overexpression of BglJ and LeuO in Escherichia coli K12
GSE3504922389370download41839Analysis of ethanologenic E.coli strain GLBRCE1 during fermentation of alkaline-pretreated corn stover hydrolysate

[HT networks based on individual high-throughput protein-protein interaction data sets]
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Reference (PMID)Edge list download#linkExperiment description
15690043download3446Large-scale APMS (Butland et al. Nature 2005)
16606699download6483Genome-scale APMS (Arifuzzaman et al. Genome Res. 2006)
19402753download5959Large-scale APMS (Hu et al. PLoS Biol. 2009)
24561554download1106Large-scale yeast two-hybrid (Y2H) screen (Rajagopala et al. Nat Biotechnol. 2014)


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