Organism : Geobacter sulfurreducens | Module List :
GSU1887 rpoN

RNA polymerase sigma-54 factor (NCBI)

CircVis
Functional Annotations (12)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 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
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1887
(Mouseover regulator name to see its description)

GSU1887 is regulated by 17 influences and regulates 8 modules.
Regulators for GSU1887 rpoN (17)
Regulator Module Operator
GSU0372 50 tf
GSU1887 50 tf
GSU2033 50 tf
GSU2506 50 tf
GSU2915 50 tf
GSU3421 50 tf
GSU3457 50 tf
GSU0079 238 tf
GSU0266 238 tf
GSU0366 238 tf
GSU0736 238 tf
GSU1887 238 tf
GSU2202 238 tf
GSU2237 238 tf
GSU2524 238 tf
GSU2698 238 tf
GSU2831 238 tf

Warning: GSU1887 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
2260 8.30e-01 caAaTgtTTGactTgAcagGc.G
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2261 9.80e+00 tAttCCacaaCaGgGgt.ggGGGA
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2636 8.60e-06 tttATattttT.TaagGtgTga
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2637 1.90e-04 AaAAcGtcactGaCGcataAAAA
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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 GSU1887

GSU1887 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 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
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
Module neighborhood information for GSU1887

GSU1887 has total of 43 gene neighbors in modules 50, 238
Gene neighbors (43)
Gene Common Name Description Module membership
GSU0038 GSU0038 lipoprotein, putative (VIMSS) 50, 267
GSU0099 GSU0099 MglA protein (VIMSS) 50, 62
GSU0455 GSU0455 rare lipoprotein A domain protein (VIMSS) 50, 228
GSU0505 GSU0505 rhodanese-like domain protein (VIMSS) 228, 238
GSU0507 GSU0507 membrane protein, putative (NCBI) 18, 238
GSU0643 rpsP ribosomal protein S16 (NCBI) 50, 62
GSU0734 GSU0734 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0735 GSU0735 PTS system IIA component, fructose subfamily (VIMSS) 238, 276
GSU0736 GSU0736 pemK protein, putative (VIMSS) 238, 265
GSU0739 GSU0739 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0740 GSU0740 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0741 GSU0741 NAD-dependent dehydrogenase subunit (VIMSS) 238, 265
GSU0744 GSU0744 hypothetical protein (VIMSS) 238, 265
GSU0745 GSU0745 NAD-dependent dehydrogenase subunit (NCBI) 178, 238
GSU0826 GSU0826 hypothetical protein (VIMSS) 228, 238
GSU0851 GSU0851 rhomboid family protein (VIMSS) 32, 238
GSU0869 GSU0869 LysM domain/NLP/P60 family protein (NCBI) 50, 228
GSU0871 GSU0871 radical SAM domain protein/B12 binding domain protein (NCBI) 50, 169
GSU0978 GSU0978 hypothetical protein (NCBI) 50, 268
GSU1233 GSU1233 phosphoesterase, putative (NCBI) 11, 50
GSU1627 secG preprotein translocase, SecG subunit (NCBI) 26, 238
GSU1628 GSU1628 phosphoglycerate kinase/triosephosphate isomerase (VIMSS) 214, 238
GSU1629 gap glyceraldehyde 3-phosphate dehydrogenase 1 (NCBI) 62, 238
GSU1630 GSU1630 sensory box histidine kinase (VIMSS) 238, 327
GSU1826 GSU1826 lytic murein transglycosylase, putative (VIMSS) 50, 267
GSU1886 yfiA ribosomal subunit interface protein (NCBI) 169, 238
GSU1887 rpoN RNA polymerase sigma-54 factor (NCBI) 50, 238
GSU1888 GSU1888 ABC transporter, ATP-binding protein (VIMSS) 50, 228
GSU1889 GSU1889 conserved hypothetical protein (VIMSS) 50, 228
GSU1890 GSU1890 hypothetical protein (VIMSS) 50, 228
GSU2223 cheY-6 chemotaxis protein CheY (NCBI) 101, 238
GSU2621 spoIID stage II sporulation-related protein (NCBI) 50, 228
GSU3135 lspA lipoprotein signal peptidase (NCBI) 77, 238
GSU3136 ileS isoleucyl-tRNA synthetase (NCBI) 228, 238
GSU3237 GSU3237 hypothetical protein (VIMSS) 116, 238
GSU3243 GSU3243 hypothetical protein (VIMSS) 50, 228
GSU3318 GSU3318 conserved hypothetical protein (VIMSS) 11, 50
GSU3320 prmA ribosomal protein L11 methyltransferase, putative (NCBI) 11, 50
GSU3321 GSU3321 phosphoglucomutase/phosphomannomutase family protein (VIMSS) 11, 50
GSU3322 corA-2 magnesium and cobalt transport protein CorA (NCBI) 11, 50
GSU3339 groES chaperonin, 10 kDa (NCBI) 50, 238
GSU3340 groeL 60 kDa chaperonin (NCBI) 50, 228
GSU3453 hemE uroporphyrinogen decarboxylase (NCBI) 50, 228
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 GSU1887
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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