Organism : Geobacter sulfurreducens | Module List :
GSU0655 rpoH

RNA polymerase sigma-32 factor (NCBI)

CircVis
Functional Annotations (13)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
response to heat go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
rpoH_proteo tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0655
(Mouseover regulator name to see its description)

GSU0655 is regulated by 16 influences and regulates 20 modules.
Regulators for GSU0655 rpoH (16)
Regulator Module Operator
GSU0399 298 tf
GSU0655 298 tf
GSU0811 298 tf
GSU1250 298 tf
GSU1639 298 tf
GSU2666 298 tf
GSU2915 298 tf
GSU0207 57 tf
GSU0655 57 tf
GSU1095 57 tf
GSU1250 57 tf
GSU1268 57 tf
GSU1934 57 tf
GSU2041 57 tf
GSU2670 57 tf
GSU2741 57 tf

Warning: GSU0655 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
2274 2.40e-01 ta.TtCaActc.aTAgaTg.TgcA
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2275 1.70e+02 cccGG.tgcaGgggaaaCAa
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2754 9.30e+02 cTcCcCgcTTTtc
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2755 5.70e+03 GTtcCGgtggAGg
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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 GSU0655

GSU0655 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
response to heat go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
rpoH_proteo tigr/ tigrfam
Module neighborhood information for GSU0655

GSU0655 has total of 37 gene neighbors in modules 57, 298
Gene neighbors (37)
Gene Common Name Description Module membership
GSU0026 GSU0026 TonB-dependent receptor, putative (VIMSS) 57, 184
GSU0027 GSU0027 TolR protein (VIMSS) 57, 266
GSU0029 GSU0029 hydrolase, carbon-nitrogen family (VIMSS) 57, 184
GSU0033 dnaK chaperone protein dnaK (NCBI) 57, 184
GSU0034 dnaJ chaperone protein dnaJ (NCBI) 57, 184
GSU0235 GSU0235 S1 RNA binding domain protein (VIMSS) 59, 298
GSU0371 GSU0371 carbohydrate phosphorylase family protein (VIMSS) 25, 57
GSU0495 GSU0495 hypothetical protein (VIMSS) 57, 303
GSU0655 rpoH RNA polymerase sigma-32 factor (NCBI) 57, 298
GSU0811 ntrX nitrogen regulation protein NtrX (NCBI) 71, 298
GSU0863 GSU0863 conserved hypothetical protein (VIMSS) 57, 253
GSU0928 GSU0928 peptidase, M16 family (NCBI) 20, 57
GSU1035 GSU1035 methyl-accepting chemotaxis protein (NCBI) 57, 189
GSU1072 GSU1072 transcriptional regulator, IclR family (VIMSS) 57, 135
GSU1081 GSU1081 conserved hypothetical protein (VIMSS) 202, 298
GSU1083 GSU1083 conserved hypothetical protein (VIMSS) 57, 110
GSU1084 GSU1084 hypothetical protein (VIMSS) 57, 110
GSU1085 GSU1085 hypothetical protein (VIMSS) 57, 189
GSU1144 GSU1144 chemotaxis protein CheD, putative (VIMSS) 57, 241
GSU1326 recG ATP-dependent DNA helicase RecG (NCBI) 296, 298
GSU1370 GSU1370 oxidoreductase, aldo/keto reductase family (NCBI) 57, 321
GSU1394 GSU1394 spore coat protein-related protein (NCBI) 20, 57
GSU1395 GSU1395 hypothetical protein (VIMSS) 57, 189
GSU1479 GSU1479 conserved hypothetical protein (VIMSS) 57, 292
GSU1677 GSU1677 AMP-binding enzyme/acyltransferase (NCBI) 57, 66
GSU1720 GSU1720 6-pyruvoyl tetrahydrobiopterin synthase family protein (NCBI) 57, 125
GSU1876 GSU1876 hypothetical protein (VIMSS) 194, 298
GSU1947 GSU1947 hypothetical protein (VIMSS) 57, 292
GSU2417 GSU2417 hypothetical protein (VIMSS) 57, 135
GSU2420 GSU2420 ferredoxin family protein (VIMSS) 57, 293
GSU2459 GSU2459 hypothetical protein (VIMSS) 57, 179
GSU2525 GSU2525 nitroreductase family protein (VIMSS) 57, 307
GSU2526 GSU2526 membrane protein, putative (VIMSS) 57, 125
GSU2750 GSU2750 conserved domain protein (VIMSS) 57, 253
GSU2786 b2530 cysteine desulfurase (NCBI) 57, 78
GSU3029 GSU3029 acyltransferase family protein (NCBI) 57, 110
GSU3358 GSU3358 hypothetical protein (VIMSS) 286, 298
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 GSU0655
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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