Organism : Geobacter sulfurreducens | Module List :
GSU3089 rpoD

RNA polymerase sigma factor RpoD (NCBI)

CircVis
Functional Annotations (8)
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
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
RpoD_Cterm tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3089
(Mouseover regulator name to see its description)

GSU3089 is regulated by 17 influences and regulates 13 modules.
Regulators for GSU3089 rpoD (17)
Regulator Module Operator
GSU0164 267 tf
GSU1569 267 tf
GSU1887 267 tf
GSU1905 267 tf
GSU2831 267 tf
GSU2868 267 tf
GSU2915 267 tf
GSU3089 267 tf
GSU0732 53 tf
GSU1218 53 tf
GSU1320 53 tf
GSU1525 53 tf
GSU1692 53 tf
GSU1989 53 tf
GSU1992 53 tf
GSU2945 53 tf
GSU3089 53 tf

Warning: GSU3089 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
2266 6.10e+02 taaaGTTctTacagg
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2267 2.40e+03 aAAATCAaaCaAcTgC.AA
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2694 3.30e-05 TTTttaTTgaCAa.C
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2695 4.20e+03 aagAcaaTgaC
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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 GSU3089

GSU3089 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
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
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
RpoD_Cterm tigr/ tigrfam
Module neighborhood information for GSU3089

GSU3089 has total of 47 gene neighbors in modules 53, 267
Gene neighbors (47)
Gene Common Name Description Module membership
GSU0038 GSU0038 lipoprotein, putative (VIMSS) 50, 267
GSU0144 GSU0144 sensory box histidine kinase (VIMSS) 53, 85
GSU0304 pepN aminopeptidase N (NCBI) 53, 290
GSU0500 typA GTP-binding protein TypA (NCBI) 53, 320
GSU0647 GSU0647 conserved hypothetical protein (VIMSS) 154, 267
GSU0648 rplS ribosomal protein L19 (NCBI) 228, 267
GSU0657 GSU0657 hypothetical protein (VIMSS) 53, 315
GSU0681 GSU0681 sensory box histidine kinase (VIMSS) 53, 85
GSU0827 GSU0827 hypothetical protein (VIMSS) 27, 53
GSU0829 GSU0829 heavy metal efflux pump, CzcB family (VIMSS) 27, 53
GSU1036 GSU1036 sensor histidine kinase (VIMSS) 53, 157
GSU1114 GSU1114 TPR domain protein (VIMSS) 181, 267
GSU1115 GSU1115 transcriptional regulator, putative (VIMSS) 56, 267
GSU1116 GSU1116 conserved domain protein (VIMSS) 212, 267
GSU1414 GSU1414 sensory box histidine kinase/response regulator (VIMSS) 53, 275
GSU1427 GSU1427 anti-anti-sigma factor (VIMSS) 53, 268
GSU1430 GSU1430 hypothetical protein (VIMSS) 53, 229
GSU1598 GSU1598 conserved hypothetical protein (NCBI) 35, 267
GSU1642 GSU1642 conserved hypothetical protein (VIMSS) 27, 53
GSU1673 GSU1673 hypothetical protein (VIMSS) 53, 200
GSU1817 GSU1817 outer membrane lipoprotein, Slp family, putative (VIMSS) 53, 264
GSU1825 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (VIMSS) 35, 267
GSU1826 GSU1826 lytic murein transglycosylase, putative (VIMSS) 50, 267
GSU1857 GSU1857 hypothetical protein (VIMSS) 53, 203
GSU1989 GSU1989 sigma-54 dependent DNA-binding response regulator (VIMSS) 53, 268
GSU1990 GSU1990 sensor histidine kinase (VIMSS) 53, 200
GSU2238 gmk guanylate kinase (NCBI) 140, 267
GSU2665 GSU2665 efflux transporter, RND family, MFP subunit (NCBI) 53, 244
GSU2666 GSU2666 transcriptional regulator, TetR family (VIMSS) 53, 244
GSU2668 GSU2668 hypothetical protein (VIMSS) 53, 244
GSU2669 GSU2669 sensor histidine kinase (VIMSS) 53, 244
GSU2678 hsp heat shock protein, Hsp20 family (NCBI) 53, 200
GSU2692 GSU2692 immunogenic protein family protein (VIMSS) 53, 194
GSU2875 rpsI ribosomal protein S9 (NCBI) 58, 267
GSU2876 rplM ribosomal protein L13 (NCBI) 58, 267
GSU3074 murE UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate ligase (NCBI) 200, 267
GSU3075 GSU3075 penicillin-binding protein (VIMSS) 200, 267
GSU3077 mraW S-adenosyl-methyltransferase MraW (NCBI) 200, 267
GSU3078 GSU3078 mraZ protein, putative (NCBI) 200, 267
GSU3086 GSU3086 conserved hypothetical protein (VIMSS) 53, 258
GSU3088 GSU3088 ybaK/ebsC protein (VIMSS) 53, 324
GSU3089 rpoD RNA polymerase sigma factor RpoD (NCBI) 53, 267
GSU3090 dnaG DNA primase (NCBI) 200, 267
GSU3092 GSU3092 YqeY family protein (VIMSS) 58, 267
GSU3095 hisF imidazoleglycerol phosphate synthase, cyclase subunit (NCBI) 53, 99
GSU3139 GSU3139 conserved hypothetical protein (VIMSS) 53, 216
GSU3467 GSU3467 conserved hypothetical protein TIGR00278 (VIMSS) 116, 267
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 GSU3089
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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