Organism : Geobacter sulfurreducens | Module List :
GSU2185

flgM family protein (VIMSS)

CircVis
Functional Annotations (5)
Function System
transcription repressor activity go/ molecular_function
flagellum go/ cellular_component
negative regulation of transcription, DNA-dependent go/ biological_process
Flagellar assembly kegg/ kegg pathway
FlgM_jcvi tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2185
(Mouseover regulator name to see its description)

GSU2185 is regulated by 16 influences and regulates 15 modules.
Regulators for GSU2185 (16)
Regulator Module Operator
GSU0018 114 tf
GSU0191 114 tf
GSU0205 114 tf
GSU0551 114 tf
GSU1270 114 tf
GSU2185 114 tf
GSU0284 321 tf
GSU0534 321 tf
GSU0655 321 tf
GSU0776 321 tf
GSU1934 321 tf
GSU2185 321 tf
GSU2571 321 tf
GSU2587 321 tf
GSU2670 321 tf
GSU2926 321 tf

Warning: GSU2185 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
2388 7.20e-06 aTgtTatt.tTttAt
Loader icon
2389 4.30e+03 gTAGaaAAA
Loader icon
2798 1.30e+03 CCttGaggAAAaagG
Loader icon
2799 6.90e+04 AAtcgaCaCAaAA
Loader icon
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 GSU2185

GSU2185 is enriched for 5 functions in 4 categories.
Enrichment Table (5)
Function System
transcription repressor activity go/ molecular_function
flagellum go/ cellular_component
negative regulation of transcription, DNA-dependent go/ biological_process
Flagellar assembly kegg/ kegg pathway
FlgM_jcvi tigr/ tigrfam
Module neighborhood information for GSU2185

GSU2185 has total of 52 gene neighbors in modules 114, 321
Gene neighbors (52)
Gene Common Name Description Module membership
GSU0098 GSU0098 MglB protein (VIMSS) 114, 264
GSU0130 fmt methionyl-tRNA formyltransferase (NCBI) 172, 321
GSU0211 GSU0211 ABC transporter, permease protein, putative (VIMSS) 46, 321
GSU0460 fabF-1 3-oxoacyl-(acyl-carrier-protein) synthase II (NCBI) 40, 114
GSU0501 GSU0501 lipoprotein, putative (VIMSS) 114, 121
GSU0535 cysK cysteine synthase A (NCBI) 290, 321
GSU0765 GSU0765 hypothetical protein (VIMSS) 103, 321
GSU0782 GSU0782 nickel-dependent hydrogenase, small subunit (VIMSS) 114, 273
GSU0783 GSU0783 nickel-dependent hydrogenase, iron-sulfur cluster-binding protein (VIMSS) 114, 273
GSU0784 GSU0784 nickel-dependent hydrogenase, membrane protein (VIMSS) 114, 159
GSU0785 GSU0785 nickel-dependent hydrogenase, large subunit (VIMSS) 114, 273
GSU0786 GSU0786 hydrogenase maturation protease (VIMSS) 114, 273
GSU0787 GSU0787 twin-arginine translocation protein, TatA/E family (NCBI) 114, 159
GSU0788 GSU0788 conserved hypothetical protein (VIMSS) 114, 159
GSU0794 GSU0794 pyridine nucleotide-disulfide oxidoreductase/rhodanese domain protein (NCBI) 114, 202
GSU0856 htpX peptidase, M48 family (NCBI) 71, 321
GSU0874 GSU0874 hypothetical protein (VIMSS) 46, 321
GSU1087 GSU1087 conserved hypothetical protein (VIMSS) 110, 114
GSU1239 gltB glutamate synthase-related protein (NCBI) 114, 202
GSU1337 GSU1337 hypothetical protein (VIMSS) 203, 321
GSU1370 GSU1370 oxidoreductase, aldo/keto reductase family (NCBI) 57, 321
GSU1373 GSU1373 hypothetical protein (VIMSS) 59, 321
GSU1402 accA acetyl-CoA carboxylase, carboxyl transferase, alpha subunit (NCBI) 20, 321
GSU1528 GSU1528 ABC transporter, periplasmic substrate-binding protein (VIMSS) 114, 159
GSU1656 GSU1656 sensory box/response regulator (VIMSS) 17, 114
GSU1699 GSU1699 TonB-dependent receptor, putative (VIMSS) 38, 321
GSU1765 SelGGPS geranyltranstransferase (NCBI) 292, 321
GSU1937 GSU1937 GGDEF domain/HAMP domain protein (NCBI) 203, 321
GSU1939 GSU1939 GAF domain/His Kinase A domain/HD domain protein (NCBI) 114, 203
GSU2082 GSU2082 conserved hypothetical protein (VIMSS) 253, 321
GSU2100 katG catalase/peroxidase (NCBI) 65, 321
GSU2184 GSU2184 polyA polymerase family protein (NCBI) 38, 321
GSU2185 GSU2185 flgM family protein (VIMSS) 114, 321
GSU2190 GSU2190 class II Aldolase and Adducin N-terminal domain protein (NCBI) 309, 321
GSU2196 GSU2196 hydrolase, putative (VIMSS) 203, 321
GSU2198 miaB tRNA-i(6)A37 modification enzyme MiaB (NCBI) 203, 321
GSU2218 cheW-6 chemotaxis protein CheW (NCBI) 59, 321
GSU2290 pncA pyrazinamidase/nicotinamidase, putative (NCBI) 46, 321
GSU2394 GSU2394 hypothetical protein (VIMSS) 321, 336
GSU2442 GSU2442 RelA/SpoT domain protein (NCBI) 114, 200
GSU2541 proC pyrroline-5-carboxylate reductase (NCBI) 114, 304
GSU2700 GSU2700 tungstate ABC transporter, periplasmic tungstate-binding protein, putative (NCBI) 114, 319
GSU2793 GSU2793 hypothetical protein (VIMSS) 114, 187
GSU2797 etfB electron transfer flavoprotein, beta subunit (NCBI) 114, 235
GSU2920 GSU2920 hypothetical protein (VIMSS) 38, 321
GSU2930 GSU2930 cytochrome c family protein (VIMSS) 253, 321
GSU3111 GSU3111 hypothetical protein (VIMSS) 290, 321
GSU3211 proA gamma-glutamyl phosphate reductase (NCBI) 160, 321
GSU3295 GSU3295 conserved hypothetical protein (VIMSS) 38, 321
GSU3296 GSU3296 glycolate oxidase subunit GlcD, putative (VIMSS) 38, 321
GSU3297 GSU3297 iron-sulfur cluster-binding protein (NCBI) 38, 321
GSU3348 hslO chaperonin, 33 kDa family (NCBI) 46, 321
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 GSU2185
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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