Organism : Geobacter sulfurreducens | Module List :
GSU0721

RNA polymerase sigma-E factor, putative (NCBI)

CircVis
Functional Annotations (11)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog 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
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0721
(Mouseover regulator name to see its description)

GSU0721 is regulated by 19 influences and regulates 12 modules.
Regulators for GSU0721 (19)
Regulator Module Operator
GSU0041 150 tf
GSU0178 150 tf
GSU0366 150 tf
GSU0721 150 tf
GSU0770 150 tf
GSU1653 150 tf
GSU2817 150 tf
GSU2987 150 tf
GSU3127 150 tf
GSU0031 194 tf
GSU0581 194 tf
GSU0721 194 tf
GSU1201 194 tf
GSU1483 194 tf
GSU1831 194 tf
GSU2753 194 tf
GSU2964 194 tf
GSU3089 194 tf
GSU3396 194 tf

Warning: GSU0721 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
2460 3.10e+01 GcAaaGgaGCc
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2461 2.10e+02 GGcGcCttTtTcggt
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2548 4.10e+03 TatcGC.ggcactACgAacA
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2549 7.30e+04 CcgGgAAgcGT
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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 GSU0721

GSU0721 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog 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
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
sigma70-ECF tigr/ tigrfam
Module neighborhood information for GSU0721

GSU0721 has total of 33 gene neighbors in modules 150, 194
Gene neighbors (33)
Gene Common Name Description Module membership
GSU0140 GSU0140 conserved hypothetical protein (VIMSS) 150, 251
GSU0141 GSU0141 conserved hypothetical protein (NCBI) 150, 280
GSU0142 pgpA phosphatidylglycerophosphatase A (NCBI) 187, 194
GSU0173 GSU0173 conserved hypothetical protein (VIMSS) 194, 240
GSU0203 GSU0203 conserved hypothetical protein (VIMSS) 194, 234
GSU0485 GSU0485 conserved hypothetical protein (VIMSS) 100, 194
GSU0711 GSU0711 endonuclease/exonuclease/phosphatase family protein (NCBI) 194, 240
GSU0721 GSU0721 RNA polymerase sigma-E factor, putative (NCBI) 150, 194
GSU0722 GSU0722 hypothetical protein (VIMSS) 72, 150
GSU0723 GSU0723 conserved hypothetical protein (VIMSS) 150, 165
GSU0725 GSU0725 hypothetical protein (VIMSS) 150, 187
GSU0936 GSU0936 glutamine amidotransferase, class I (NCBI) 150, 280
GSU0937 nifV homocitrate synthase (NCBI) 64, 150
GSU0938 GSU0938 hypothetical protein (VIMSS) 64, 150
GSU1099 pstS phosphate ABC transporter, periplasmic phosphate-binding protein (NCBI) 150, 246
GSU1426 GSU1426 rsbW protein, putative (VIMSS) 127, 194
GSU1876 GSU1876 hypothetical protein (VIMSS) 194, 298
GSU2077 GSU2077 hypothetical protein (VIMSS) 59, 194
GSU2471 GSU2471 group II intron, maturase (VIMSS) 150, 194
GSU2692 GSU2692 immunogenic protein family protein (VIMSS) 53, 194
GSU2794 mscL large conductance mechanosensitive channel protein (NCBI) 187, 194
GSU2799 GSU2799 radical SAM domain protein (NCBI) 64, 150
GSU2800 draG dinitrogenase reductase activating glycohydrolase (NCBI) 150, 187
GSU2802 dRAT NAD(+)--dinitrogen-reductase ADP-D-ribosyltransferase (NCBI) 64, 150
GSU2806 nifEN nitrogenase molybdenum-iron cofactor biosynthesis protein NifEN (NCBI) 64, 150
GSU2820 nifD nitrogenase molybdenum-iron protein, alpha chain (NCBI) 64, 150
GSU2821 nifH nitrogenase iron protein (VIMSS) 64, 150
GSU2962 modA molybdenum ABC transporter, periplasmic molybdenum-binding protein modA (NCBI) 64, 150
GSU2963 modD additional component of molybdate ABC transporter (Dmitry Rodionov) 150, 187
GSU2965 GSU2965 conserved hypothetical protein (NCBI) 150, 235
GSU3036 fliS flagellar protein FliS (NCBI) 150, 216
GSU3037 fliD flagellar hook-associated protein 2 (NCBI) 150, 230
GSU3105 GSU3105 conserved hypothetical protein (VIMSS) 194, 256
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 GSU0721
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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