Original article Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12

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Original article Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12

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by Socorro Gama-castro , Fabio Rinaldi , Simon Clematide , Tilia Renate Ellendorff , Alberto Santos-zavaleta , Hernani Marques-madeira

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133	DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide. - Zheng, Wang, et al. - 2001 (Show Context) Citation Context ...) S180 OxyR [þ] katG Evidence PMID:2693740 (20) S99 OxyR [?] katG PMID:8990289 (21) S141 OxyR [?] katG PMID:8990289 (21) S106 OxyR [þ] katG PMID:9324269 (22) S27 OxyR [þ] katG Reference PMID:11443091 =-=(23)-=- S25 OxyR [þ] katG Reference PMID:11443092 (24) S94 OxyR [?] katG Evidence PMID:22539721 (25) S118 OxyR [þ] katG Figure/Table PMID:22539721 (25) S20 H202 [þ] katG Reference PMID:3045098 (26) S20 OxyR ...
109	Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation,” - Storz, Tartaglia, et al. - 1990 (Show Context) Citation Context ...egulation of gene expression by OxyR, the transcriptional regulator for the expression of antioxidant genes in response to oxidative stress and, in particular, to elevated levels of hydrogen peroxide =-=(6, 7)-=-. OntoGene/ODIN has been customized for the curation of gene regulation in E. coli. The set of selected papers were processed and made available to curators in the OntoGene/ODIN interface. The curator...
93	The dps promoter is activated by OxyR during growth and by IHF and sigma S in stationary phase. - Altuvia, Almiron, et al. - 1994 (Show Context) Citation Context ...igure/Table PMID:22539721 (25) S20 H202 [þ] katG Reference PMID:3045098 (26) S20 OxyR [þ] katG Reference PMID:3045098 (26) S34 OxyR [?] katG Reference PMID:7868602 (27) S15 OxyR [?] katG PMID:7984106 =-=(28)-=- S91 OxyR [?] katG Reference linked PMID:7984106 (28) S135 OxyR [?] katG Reference/evidence linked PMID:8087856 (29) The first column contains the ID of each sentence within the paper with PMID shown ...
91	Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: a mechanism for differential promoter selection. - Toledano - 1994 (Show Context) Citation Context ...8 (26) S34 OxyR [?] katG Reference PMID:7868602 (27) S15 OxyR [?] katG PMID:7984106 (28) S91 OxyR [?] katG Reference linked PMID:7984106 (28) S135 OxyR [?] katG Reference/evidence linked PMID:8087856 =-=(29)-=- The first column contains the ID of each sentence within the paper with PMID shown in the last column followed by their citation number in this paper. The third column indicates whether the sentence ...
84	OxyR and SoxRS regulation of fur. - Zheng, Doan, et al. - 1999 (Show Context) Citation Context ...ed to an effect found in a sentence with a GC Table 6. The (OxyRþ katG) sentences in the corpus Sentence_ID Normalized structures Information within the sentence Paper S23 OxyR [þ] katG PMID:10419964 =-=(15)-=- S17 OxyR [þ] katG PMID:12644490 (16) S165 OxyR [þ] katG Reference (PMID:2693740) PMID:12644490 (16) S116 OxyR [þ] katG PMID:15009899 (17) S38 OxyR [þ] katG Reference (PMID:2693740) PMID:1730735 (18) ...
54	Mutational analysis of the redox-sensitive transcriptional regulator OxyR: regions important for DNA binding and multimerization. - Kullik, Stevens, et al. - 1995 (Show Context) Citation Context ...llow OxyR to repress the oxyR and mom promoters during normal growth, while activating Page 3 of 13 Database, Vol. 2014, Article ID bau049 katG, ahpCF, dps, gorA, and oxyS only upon oxidative stress’ =-=(9)-=-. Note that our mapping rules associate a specific sentence with the most complete possible structure. However, as shown, a single sentence may instantiate different structures with different regulato...
43	RegulonDB: a database on transcriptional regulon in Escherichia coli, - Huerta, Salgado, et al. - 1998 (Show Context) Citation Context ...15 years ago containing high-quality manually curated knowledge on, the regulation of transcription initiation in Escherichia coli K-12, the microbial organism with the largest corpus of publications =-=(1, 2)-=-. RegulonDB contains objects such as genes, promoters, transcription factors (TFs), transcription factor binding sites (TFBSs), terminators and operons. It also contains relationships of regulation am...
41	Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress - Tartaglia, Storz, et al. - 1989 (Show Context) Citation Context ...0) PMID:1730735 (18) S208 OxyR [þ] katG Reference PMID:1730735 (18) S147 OxyR [þ] katG Reference (PMID:8087856) PMID:17464064 (19) S157 OxyR [þ] katG PMID:17464064 (19) S42 OxyR [?] katG PMID:2693740 =-=(20)-=- S140 OxyR [þ] katG PMID:2693740 (20) S180 OxyR [þ] katG Evidence PMID:2693740 (20) S99 OxyR [?] katG PMID:8990289 (21) S141 OxyR [?] katG PMID:8990289 (21) S106 OxyR [þ] katG PMID:9324269 (22) S27 Ox...
40	Demple B: Homeostatic regulation of intracellular hydrogen peroxide concentration in aerobically growing Escherichia coli. - Gonzalez-Flecha - 1997 (Show Context) Citation Context ...464064 (19) S157 OxyR [þ] katG PMID:17464064 (19) S42 OxyR [?] katG PMID:2693740 (20) S140 OxyR [þ] katG PMID:2693740 (20) S180 OxyR [þ] katG Evidence PMID:2693740 (20) S99 OxyR [?] katG PMID:8990289 =-=(21)-=- S141 OxyR [?] katG PMID:8990289 (21) S106 OxyR [þ] katG PMID:9324269 (22) S27 OxyR [þ] katG Reference PMID:11443091 (23) S25 OxyR [þ] katG Reference PMID:11443092 (24) S94 OxyR [?] katG Evidence PMID...
28	EcoCyc: fusing model organism databases with systems biology,” Nucleic acids research - Keseler, Mackie, et al. - 2013 (Show Context) Citation Context ...fic term. Synonyms are also used for TFs and gene names. We used the same mapping of synonyms to the main name of the gene or TF based on the names of objects commonly used in RegulonDB and in EcoCyc =-=(12)-=-. Having solved the problems of the variety of sentences with the same meaning and synonyms for elements involved in RIs, we were able to initiate the analysis of the content of all the informative se...
25	Nucleotide sequence of katG, encoding catalase HPI of Escherichia coli. - Triggs-Raine, Doble, et al. - 1988 (Show Context) Citation Context ...:11443091 (23) S25 OxyR [þ] katG Reference PMID:11443092 (24) S94 OxyR [?] katG Evidence PMID:22539721 (25) S118 OxyR [þ] katG Figure/Table PMID:22539721 (25) S20 H202 [þ] katG Reference PMID:3045098 =-=(26)-=- S20 OxyR [þ] katG Reference PMID:3045098 (26) S34 OxyR [?] katG Reference PMID:7868602 (27) S15 OxyR [?] katG PMID:7984106 (28) S91 OxyR [?] katG Reference linked PMID:7984106 (28) S135 OxyR [?] katG...
23	Redox regulation of OxyR requires specific disulfide bond formation involving a rapid kinetic reaction path. - Lee, Lee, et al. - 2004 (Show Context) Citation Context ...egulation of gene expression by OxyR, the transcriptional regulator for the expression of antioxidant genes in response to oxidative stress and, in particular, to elevated levels of hydrogen peroxide =-=(6, 7)-=-. OntoGene/ODIN has been customized for the curation of gene regulation in E. coli. The set of selected papers were processed and made available to curators in the OntoGene/ODIN interface. The curator...
23	Induction of the sufA operon encoding Fe-S assembly proteins by superoxide generators and hydrogen peroxide: involvement of OxyR, IHF and an unidentified oxidant-responsive factor, Molecular microbiology 51 - Lee, Yeo, et al. - 2004 (Show Context) Citation Context ...ion within the sentence Paper S23 OxyR [þ] katG PMID:10419964 (15) S17 OxyR [þ] katG PMID:12644490 (16) S165 OxyR [þ] katG Reference (PMID:2693740) PMID:12644490 (16) S116 OxyR [þ] katG PMID:15009899 =-=(17)-=- S38 OxyR [þ] katG Reference (PMID:2693740) PMID:1730735 (18) S208 OxyR [þ] katG Reference PMID:1730735 (18) S147 OxyR [þ] katG Reference (PMID:8087856) PMID:17464064 (19) S157 OxyR [þ] katG PMID:1746...
21	RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more - Salgado - 2013 (Show Context) Citation Context ...15 years ago containing high-quality manually curated knowledge on, the regulation of transcription initiation in Escherichia coli K-12, the microbial organism with the largest corpus of publications =-=(1, 2)-=-. RegulonDB contains objects such as genes, promoters, transcription factors (TFs), transcription factor binding sites (TFBSs), terminators and operons. It also contains relationships of regulation am...
15	Computation-directed identification of OxyR DNA binding sites in Escherichia coli. - Zheng, Wang, et al. - 2001 (Show Context) Citation Context ... S99 OxyR [?] katG PMID:8990289 (21) S141 OxyR [?] katG PMID:8990289 (21) S106 OxyR [þ] katG PMID:9324269 (22) S27 OxyR [þ] katG Reference PMID:11443091 (23) S25 OxyR [þ] katG Reference PMID:11443092 =-=(24)-=- S94 OxyR [?] katG Evidence PMID:22539721 (25) S118 OxyR [þ] katG Figure/Table PMID:22539721 (25) S20 H202 [þ] katG Reference PMID:3045098 (26) S20 OxyR [þ] katG Reference PMID:3045098 (26) S34 OxyR [...
11	Transcriptional regulation of the Escherichia coli oxyR gene as a function of cell growth. - Gonzalez-Flecha, Demple - 1997 (Show Context) Citation Context ...693740 (20) S140 OxyR [þ] katG PMID:2693740 (20) S180 OxyR [þ] katG Evidence PMID:2693740 (20) S99 OxyR [?] katG PMID:8990289 (21) S141 OxyR [?] katG PMID:8990289 (21) S106 OxyR [þ] katG PMID:9324269 =-=(22)-=- S27 OxyR [þ] katG Reference PMID:11443091 (23) S25 OxyR [þ] katG Reference PMID:11443092 (24) S94 OxyR [?] katG Evidence PMID:22539721 (25) S118 OxyR [þ] katG Figure/Table PMID:22539721 (25) S20 H202...
10	Multidegenerate DNA recognition by the OxyR transcriptional regulator - Tartaglia, Gimeno, et al. - 1992 (Show Context) Citation Context ... (15) S17 OxyR [þ] katG PMID:12644490 (16) S165 OxyR [þ] katG Reference (PMID:2693740) PMID:12644490 (16) S116 OxyR [þ] katG PMID:15009899 (17) S38 OxyR [þ] katG Reference (PMID:2693740) PMID:1730735 =-=(18)-=- S208 OxyR [þ] katG Reference PMID:1730735 (18) S147 OxyR [þ] katG Reference (PMID:8087856) PMID:17464064 (19) S157 OxyR [þ] katG PMID:17464064 (19) S42 OxyR [?] katG PMID:2693740 (20) S140 OxyR [þ] k...
9	The Escherichia coli MntR miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis - LS, Sandoval, et al. (Show Context) Citation Context ...ds as follows: the MntR TF positively regulates the expression of the mntH gene in the presence of manganese. Table 1 illustrates four different instances of this semantic structure in the same paper =-=(8)-=-. A total of 898 instantiated structures were derived from the 43 papers. It should be noted that the relationship between a sentence of a paper and its corresponding structure is not always going to ...
8	COLOMBOS v2.0: an ever expanding collection of bacterial expression compendia. - Meysman - 2014 (Show Context) Citation Context ...evels of detail used to describe GCs. Efforts such as those of COLOMBOS and PortEco, dealing with repositories of microarray experimental data, use either use previous ontologies or develop their own =-=(10, 11)-=-. Thanks to an initial collaboration with the COLOMBOS team, we are using their descriptions as an alternative dictionary of conditions within ODIN (See Figure 1). For example, ‘oxidative stress’, can...
6	Purification and characterization of the Escherichia coliOxyR protein, the positive regulator for a hydrogen peroxide-inducible regulon - Tao, Makino, et al. - 1991 (Show Context) Citation Context ...at our results are correct, as the OxyR protein is normally active under the condition of ‘oxidative stress’ (6, 7). It is also active under conditions of reduction, in which case it represses itself =-=(14)-=-, which is also shown in Table 3. OxyR RIs and their GCs Interaction number GENE/operon target EFFECT GC 1 fhuF Repressor Hydrogen peroxide treatment 2 flu ‘Activator/repressor’ Hydrogen peroxide trea...
5	Using the OntoGene pipeline for the triage task of BioCreative - Rinaldi, Clematide, et al. - 2012
3	Using ODIN for a PharmGKB revalidation experiment - Rinaldi, Clematide, et al. - 2012
3	Phase variation of Ag43 is independent of the oxidation state of OxyR - Wallecha, Correnti, et al. - 2003 (Show Context) Citation Context ...ith a GC Table 6. The (OxyRþ katG) sentences in the corpus Sentence_ID Normalized structures Information within the sentence Paper S23 OxyR [þ] katG PMID:10419964 (15) S17 OxyR [þ] katG PMID:12644490 =-=(16)-=- S165 OxyR [þ] katG Reference (PMID:2693740) PMID:12644490 (16) S116 OxyR [þ] katG PMID:15009899 (17) S38 OxyR [þ] katG Reference (PMID:2693740) PMID:1730735 (18) S208 OxyR [þ] katG Reference PMID:173...
3	The Escherichia coli yhjA gene, encoding a predicted cytochrome c perodiase, is regulated by FNR and OxyR - Partridge, Poole, et al. - 2007 (Show Context) Citation Context ... OxyR [þ] katG PMID:15009899 (17) S38 OxyR [þ] katG Reference (PMID:2693740) PMID:1730735 (18) S208 OxyR [þ] katG Reference PMID:1730735 (18) S147 OxyR [þ] katG Reference (PMID:8087856) PMID:17464064 =-=(19)-=- S157 OxyR [þ] katG PMID:17464064 (19) S42 OxyR [?] katG PMID:2693740 (20) S140 OxyR [þ] katG PMID:2693740 (20) S180 OxyR [þ] katG Evidence PMID:2693740 (20) S99 OxyR [?] katG PMID:8990289 (21) S141 O...
2	Evidence classification of high-throughput protocols and confidence integration in RegulonDB.Database - Weiss, Medina-Rivera, et al. - 2013 (Show Context) Citation Context ...ur more strict curation criteria, such cases with a weak evidence are incorporated into RegulonDB only if they contain additional evidence such as the identification of the DNAbinding site for the TF =-=(13)-=-. The last of the RIs (OxyR activates the expression of genes for the unit of transcription hemF-rcsC) was found in an article that cited a work from 1994, which had escaped our curation. This showed ...
1	PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools - Hu, Sherlock, et al. - 2014 (Show Context) Citation Context ...evels of detail used to describe GCs. Efforts such as those of COLOMBOS and PortEco, dealing with repositories of microarray experimental data, use either use previous ontologies or develop their own =-=(10, 11)-=-. Thanks to an initial collaboration with the COLOMBOS team, we are using their descriptions as an alternative dictionary of conditions within ODIN (See Figure 1). For example, ‘oxidative stress’, can...
1	Endogenous protein S-Nitrosylation in Ecoli: regulation by OxyR - Seth, Hausladen, et al. - 2012 (Show Context) Citation Context ... [?] katG PMID:8990289 (21) S106 OxyR [þ] katG PMID:9324269 (22) S27 OxyR [þ] katG Reference PMID:11443091 (23) S25 OxyR [þ] katG Reference PMID:11443092 (24) S94 OxyR [?] katG Evidence PMID:22539721 =-=(25)-=- S118 OxyR [þ] katG Figure/Table PMID:22539721 (25) S20 H202 [þ] katG Reference PMID:3045098 (26) S20 OxyR [þ] katG Reference PMID:3045098 (26) S34 OxyR [?] katG Reference PMID:7868602 (27) S15 OxyR [...