Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0981

Transcriptional regulator, GntR family (NCBI)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0981
(Mouseover regulator name to see its description)

RSP_0981 is regulated by 22 influences and regulates 3 modules.
Regulators for RSP_0981 (22)
Regulator Module Operator
RSP_0395 277 tf
RSP_0402 277 tf
RSP_0623 277 tf
RSP_0981 277 tf
RSP_1191 277 tf
RSP_1669 277 tf
RSP_1739 277 tf
RSP_1776 277 tf
RSP_1892 277 tf
RSP_2130 277 tf
RSP_2494 277 tf
RSP_2965 277 tf
RSP_3001 277 tf
RSP_3448 277 tf
RSP_3700 277 tf
RSP_0087 93 tf
RSP_0395 93 tf
RSP_1231 93 tf
RSP_1590 93 tf
RSP_2171 93 tf
RSP_2494 93 tf
RSP_2922 93 tf

Warning: RSP_0981 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
7906 6.90e-11 tgtcaaTgcCTTTCcGActc
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7907 6.70e-07 aaAAaccCcgAAAaTCacGgca
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8268 1.90e-02 cagaGcAaAggcCTgAAAA
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8269 4.10e+01 cCGGAgtgTCAA.gcCTttccGA
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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_0981

RSP_0981 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for RSP_0981

RSP_0981 has total of 52 gene neighbors in modules 93, 277
Gene neighbors (52)
Gene Common Name Description Module membership
RSP_0002 spbB Histone-like nucleoid-structuring protein H-NS (NCBI) 48, 93
RSP_0125 opgG periplasmic glucan biosynthesis protein (NCBI) 277, 339
RSP_0126 RSP_0126 hypothetical protein (NCBI) 277, 339
RSP_0127 opgH Glycosyl transferase, family 2 (NCBI) 277, 339
RSP_0128 opgC OpgC protein (NCBI) 277, 339
RSP_0146 glnB Nitrogen regulatory protein P-II (NCBI) 93, 108
RSP_0147 glnA Glutamine synthetase class-I (NCBI) 25, 93
RSP_0223 RSP_0223 hypothetical protein (NCBI) 93, 358
RSP_0224 RSP_0224 ATP-dependent helicase (NCBI) 93, 358
RSP_0452 recA Recombinase A, DNA recombination protein (NCBI) 30, 93
RSP_0670 RSP_0670 Possible TolA protein (NCBI) 277, 326
RSP_0672 TolQ Biopolymer transport protein, TolQ (NCBI) 277, 286
RSP_0714 RSP_0714 hypothetical protein (NCBI) 109, 277
RSP_0797 gltX-1 Glutamyl-tRNA synthetase, class Ic (NCBI) 51, 93
RSP_0831 trpA Tryptophan synthase, alpha chain (NCBI) 51, 93
RSP_0862 leuD 3-isopropylmalate dehydratase small subunit (NCBI) 203, 277
RSP_0883 RSP_0883 SmpB protein (NCBI) 277, 279
RSP_0930 folC Folylpolyglutamate synthetase (NCBI) 130, 277
RSP_0981 RSP_0981 Transcriptional regulator, GntR family (NCBI) 93, 277
RSP_0982 RSP_0982 zinc metallopeptidases-like protein (NCBI) 93, 277
RSP_0983 RSP_0983 hypothetical protein (NCBI) 93, 277
RSP_1053 ffh Signal recognition particle protein ffh (NCBI) 210, 277
RSP_1085 RSP_1085 hypothetical protein (NCBI) 75, 93
RSP_1169 secA preprotein translocase, SecA subunit, ATPase (NCBI) 43, 277
RSP_1360 RSP_1360 hypothetical protein (NCBI) 30, 93
RSP_1383 RSP_1383 hypothetical protein (NCBI) 48, 277
RSP_1459 RSP_1459 hypothetical protein (NCBI) 93, 279
RSP_1460 RSP_1460 hypothetical protein (NCBI) 71, 93
RSP_1621 RSP_1621 Deoxyguanosinetriphosphate triphosphohydrolase-like protein (NCBI) 93, 381
RSP_1622 RSP_1622 Putative DNA-binding protein (NCBI) 93, 208
RSP_1623 RSP_1623 hypothetical protein (NCBI) 93, 130
RSP_1705 RSP_1705 Putative preprotein translocase, SecE subunit (NCBI) 75, 277
RSP_1977 cobS cobalt chelatase, CobS small subunit (NCBI) 93, 261
RSP_1978 RSP_1978 molecular chaperone, DnaJ family (NCBI) 93, 261
RSP_1979 RSP_1979 stress induced morphogen, BolA (NCBI) 93, 261
RSP_1997 lexA LexA repressor (NCBI) 30, 93
RSP_2246 hisB Imidazoleglycerol-phosphate dehydratase (NCBI) 93, 182
RSP_2329 mreB Cell shape determining protein MreB/Mrl (NCBI) 93, 309
RSP_2356 RSP_2356 hypothetical protein (NCBI) 93, 114
RSP_2361 RSP_2361 putative integrase/resolvase recombinase protein phage-related integrase (NCBI) 93, 161
RSP_2464 fabF Beta-ketoacyl synthase; 3-oxoacyl-(acyl carrier protein) synthase II (NCBI) 51, 277
RSP_2624 RSP_2624 hypothetical protein (NCBI) 30, 93
RSP_2627 hisI Phosphoribosyl-AMP cyclohydrolase (NCBI) 202, 277
RSP_2856 RSP_2856 putative oligopeptide ABC transporter, periplasmic-binding protein (NCBI) 64, 277
RSP_2981 RSP_2981 Putative protein-disulfide isomerase (NCBI) 277, 311
RSP_3003 RSP_3003 hypothetical protein (NCBI) 93, 108
RSP_3187 mdoG putative transmembrane protein (NCBI) 277, 339
RSP_3546 RSP_3546 hypothetical protein (NCBI) 47, 277
RSP_3644 RSP_3644 Metal dependent phosphohydrolase (NCBI) 93, 130
RSP_4324 RSP_4324 tRNA-Ile (NCBI) 75, 277
RSP_4325 RSP_4325 tRNA-Ala (NCBI) 75, 277
RSP_6220 RSP_6220 hypothetical protein (NCBI) 276, 277
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_0981
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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