Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0913 crt

Enoyl-CoA hydratase/isomerase (NCBI)

CircVis
Functional Annotations (18)
Function System
Enoyl-CoA hydratase/carnithine racemase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Fatty acid metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Geraniol degradation kegg/ kegg pathway
Lysine degradation kegg/ kegg pathway
Benzoate degradation kegg/ kegg pathway
Tryptophan metabolism kegg/ kegg pathway
beta-Alanine metabolism kegg/ kegg pathway
Aminobenzoate degradation kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Limonene and pinene degradation kegg/ kegg pathway
Caprolactam degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0913
(Mouseover regulator name to see its description)

RSP_0913 is regulated by 30 influences and regulates 0 modules.
Regulators for RSP_0913 crt (30)
Regulator Module Operator
RSP_0071 82 tf
RSP_0794 82 tf
RSP_0958 82 tf
RSP_0999 82 tf
RSP_1231 82 tf
RSP_2026 82 tf
RSP_2201 82 tf
RSP_3202 82 tf
RSP_3385 82 tf
RSP_0032 278 tf
RSP_0087 278 tf
RSP_0327 278 tf
RSP_0394 278 tf
RSP_0698 278 tf
RSP_0755 278 tf
RSP_0774 278 tf
RSP_0927 278 tf
RSP_1032 278 tf
RSP_1034 278 tf
RSP_1139 278 tf
RSP_1243 278 tf
RSP_1272 278 tf
RSP_1890 278 tf
RSP_2591 278 tf
RSP_2840 278 tf
RSP_3029 278 tf
RSP_3165 278 tf
RSP_3202 278 tf
RSP_3317 278 tf
RSP_3731 278 tf

Warning: RSP_0913 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7884 6.20e+00 A.ccCgCtaatTaaactGgagg
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7885 1.20e+01 aGacatcCGTCAcAT
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8270 5.40e-11 aAccGcggaAcacGttTgtCaa
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8271 6.00e-04 tc.agacTcTcCatccaaTt.ca
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_0913

RSP_0913 is enriched for 18 functions in 3 categories.
Enrichment Table (18)
Function System
Enoyl-CoA hydratase/carnithine racemase cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Fatty acid metabolism kegg/ kegg pathway
Valine leucine and isoleucine degradation kegg/ kegg pathway
Geraniol degradation kegg/ kegg pathway
Lysine degradation kegg/ kegg pathway
Benzoate degradation kegg/ kegg pathway
Tryptophan metabolism kegg/ kegg pathway
beta-Alanine metabolism kegg/ kegg pathway
Aminobenzoate degradation kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
Limonene and pinene degradation kegg/ kegg pathway
Caprolactam degradation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for RSP_0913

RSP_0913 has total of 50 gene neighbors in modules 82, 278
Gene neighbors (50)
Gene Common Name Description Module membership
RSP_0153 RSP_0153 hypothetical protein (NCBI) 107, 278
RSP_0250 RSP_0250 hypothetical protein (NCBI) 25, 278
RSP_0251 RSP_0251 Outer membrane efflux protein (NCBI) 223, 278
RSP_0252 RSP_0252 Protein-L-isoaspartatecarboxylmethyltransferase (NCBI) 262, 278
RSP_0253 RSP_0253 Glycine/D-amino acid oxidase (deaminating) (NCBI) 136, 278
RSP_0398 RSP_0398 dehydrogenase (NCBI) 239, 278
RSP_0423 RSP_0423 Aldo/keto reductase (NCBI) 121, 278
RSP_0913 crt Enoyl-CoA hydratase/isomerase (NCBI) 82, 278
RSP_0914 RSP_0914 Short-chain dehydrogenase/reductase SDR (NCBI) 82, 278
RSP_0915 RSP_0915 hypothetical protein (NCBI) 25, 278
RSP_0954 RSP_0954 Transglutaminase-like domain (NCBI) 82, 220
RSP_0958 RSP_0958 RAM domain protein (NCBI) 82, 286
RSP_1242 RSP_1242 hypothetical protein (NCBI) 76, 278
RSP_1243 RSP_1243 transcriptional regulator, LacI family (NCBI) 76, 278
RSP_1244 RSP_1244 putative IolE, Sugar phosphate isomerases/epimerases (NCBI) 76, 278
RSP_1245 RSP_1245 predicted oxidoreductase, Gfo/Idh/MocA family (NCBI) 76, 278
RSP_1247 RSP_1247 ABC sugar transporter, ATPase subunit (NCBI) 76, 278
RSP_1249 RSP_1249 ABC ribose transporter, periplasmic solute-binding protein (NCBI) 76, 278
RSP_1295 RSP_1295 putative acyl-CoA dehydrogenase (NCBI) 82, 171
RSP_1363 mepA putative murein endopeptidase transmembrane protein (NCBI) 82, 242
RSP_1374 lpsB putative lipopolysaccharide core biosynthesis mannosyltransferase protein (NCBI) 278, 308
RSP_1375 RSP_1375 hypothetical protein (NCBI) 72, 278
RSP_1492 RSP_1492 UbiH/COQ6 monooxygenase family (NCBI) 51, 278
RSP_1493 RSP_1493 Amidase (NCBI) 81, 278
RSP_1499 RSP_1499 Probable gamma-glutamyltranspeptidase (NCBI) 174, 278
RSP_1757 panC Probable pantoate--beta-alanine ligase (NCBI) 207, 278
RSP_1947 cbbJ Triosephosphate isomerase (NCBI) 278, 372
RSP_2035 RSP_2035 hypothetical protein (NCBI) 4, 82
RSP_2093 RSP_2093 Putative Mrp (Multidrug resistance-associated proteins) family protein (NCBI) 278, 329
RSP_2413 lig2 putative ATP-dependent DNA Ligase (NCBI) 82, 238
RSP_2414 RSP_2414 hypothetical protein (NCBI) 82, 280
RSP_2415 RSP_2415 hypothetical protein (NCBI) 82, 358
RSP_2416 RSP_2416 hypothetical protein (NCBI) 82, 358
RSP_2417 RSP_2417 hypothetical protein (NCBI) 82, 358
RSP_2420 RSP_2420 hypothetical protein (NCBI) 82, 133
RSP_2576 adhI Alcohol dehydrogenase class III (NCBI) 52, 278
RSP_2596 RSP_2596 ABC transporter, ATPase subunit (NCBI) 82, 338
RSP_2597 RSP_2597 ABC transporter, periplasmic substrate-binding protein (NCBI) 82, 338
RSP_2598 RSP_2598 ABC transporter, inner membrane subunit (NCBI) 82, 338
RSP_2857 RSP_2857 D-beta-hydroxybutyrate dehydrogenase (NCBI) 242, 278
RSP_3202 RSP_3202 transcriptional regulator, AraC family (NCBI) 82, 176
RSP_3275 RSP_3275 MoxR-like ATPase (NCBI) 82, 116
RSP_3276 RSP_3276 hypothetical protein (NCBI) 82, 116
RSP_3280 RSP_3280 hypothetical protein (NCBI) 82, 116
RSP_3281 RSP_3281 hypothetical protein (NCBI) 82, 116
RSP_3282 RSP_3282 hypothetical protein (NCBI) 82, 116
RSP_3316 RSP_3316 hypothetical protein (NCBI) 82, 116
RSP_3331 RSP_3331 Cupin domain containg protein (NCBI) 82, 152
RSP_3583 RSP_3583 Class I monoheme cytochrome c (NCBI) 184, 278
RSP_3833 fadB enoyl CoA hydratase (NCBI) 59, 278
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for RSP_0913
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend