Organism : Geobacter sulfurreducens | Module List :
GSU0136

membrane protein, putative (NCBI)

CircVis
Functional Annotations (1)
Function System
Predicted membrane protein cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0136
(Mouseover regulator name to see its description)

GSU0136 is regulated by 26 influences and regulates 0 modules.
Regulators for GSU0136 (26)
Regulator Module Operator
GSU0063 159 tf
GSU0205 159 tf
GSU0280 159 tf
GSU0473 159 tf
GSU1013 159 tf
GSU1495 159 tf
GSU1522 159 tf
GSU1569 159 tf
GSU1626 159 tf
GSU2041 159 tf
GSU2523 159 tf
GSU2571 159 tf
GSU2581 159 tf
GSU3363 159 tf
GSU3370 159 tf
GSU0770 36 tf
GSU1013 36 tf
GSU1419 36 tf
GSU1495 36 tf
GSU1569 36 tf
GSU2202 36 tf
GSU2571 36 tf
GSU2716 36 tf
GSU2915 36 tf
GSU3060 36 tf
GSU3387 36 tf

Warning: GSU0136 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
2232 3.50e+01 CAGggcCGgcccGAttcTcCcGAC
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2233 1.00e+04 ACGTGTctGTccAGCgcaCGA
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2478 4.70e+01 tTTtgaAga.cAAaTacAtAcacC
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2479 1.50e+03 T.aTG.CGCcGTG.T
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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 GSU0136

GSU0136 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted membrane protein cog/ cog
Module neighborhood information for GSU0136

GSU0136 has total of 34 gene neighbors in modules 36, 159
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0007 GSU0007 sensory box histidine kinase (VIMSS) 147, 159
GSU0011 GSU0011 ABC transporter, ATP-binding protein (VIMSS) 131, 159
GSU0056 GSU0056 conserved hypothetical protein (VIMSS) 36, 69
GSU0136 GSU0136 membrane protein, putative (NCBI) 36, 159
GSU0165 GSU0165 conserved hypothetical protein (VIMSS) 159, 307
GSU0189 dbpA ATP-dependent RNA helicase DbpA (NCBI) 15, 36
GSU0282 GSU0282 hypothetical protein (VIMSS) 36, 180
GSU0291 cheR CheR methyltransferase, SAM binding domain protein, putative (NCBI) 36, 296
GSU0292 GSU0292 hypothetical protein (VIMSS) 36, 84
GSU0463 GSU0463 membrane protein, putative (VIMSS) 36, 51
GSU0572 GSU0572 HAD-superfamily hydrolase, subfamily IA, variant 3 (NCBI) 47, 159
GSU0705 GSU0705 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 36, 278
GSU0784 GSU0784 nickel-dependent hydrogenase, membrane protein (VIMSS) 114, 159
GSU0787 GSU0787 twin-arginine translocation protein, TatA/E family (NCBI) 114, 159
GSU0788 GSU0788 conserved hypothetical protein (VIMSS) 114, 159
GSU0820 sppA-1 signal peptide peptidase SppA, 36K type (NCBI) 36, 79
GSU1033 GSU1033 methyl-accepting chemotaxis protein (VIMSS) 36, 198
GSU1040 GSU1040 hypothetical protein (VIMSS) 36, 76
GSU1269 GSU1269 hypothetical protein (VIMSS) 40, 159
GSU1353 GSU1353 prevent-host-death family protein (NCBI) 81, 159
GSU1354 GSU1354 plasmid stabilization system family protein (NCBI) 159, 260
GSU1385 GSU1385 conserved hypothetical protein (VIMSS) 36, 105
GSU1388 GSU1388 CRISPR-associated protein, CT1976 family (NCBI) 36, 130
GSU1528 GSU1528 ABC transporter, periplasmic substrate-binding protein (VIMSS) 114, 159
GSU1609 GSU1609 outer membrane efflux protein (VIMSS) 159, 335
GSU1924 GSU1924 IPT/TIG domain protein (VIMSS) 47, 159
GSU1941 GSU1941 sensor histidine kinase (VIMSS) 159, 335
GSU2178 GSU2178 hypothetical protein (VIMSS) 34, 36
GSU2362 GSU2362 transcriptional regulator, MarR family (VIMSS) 140, 159
GSU2440 GSU2440 hypothetical protein (VIMSS) 61, 159
GSU2579 GSU2579 methyl-accepting chemotaxis protein (VIMSS) 36, 141
GSU2684 GSU2684 hypothetical protein (VIMSS) 141, 159
GSU2777 GSU2777 transporter, LysE family (VIMSS) 36, 269
GSU3368 ispD 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (NCBI) 159, 193
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 GSU0136
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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