Organism : Geobacter sulfurreducens | Module List :
GSU2330

membrane protein, putative (VIMSS)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2330
(Mouseover regulator name to see its description)

GSU2330 is regulated by 10 influences and regulates 0 modules.
Regulators for GSU2330 (10)
Regulator Module Operator
GSU0581 175 tf
GSU0732 175 tf
GSU1218 175 tf
GSU1525 175 tf
GSU1626 175 tf
GSU1692 175 tf
GSU2581 175 tf
GSU0811 274 tf
GSU1495 274 tf
GSU3418 274 tf

Warning: GSU2330 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
2510 1.10e+03 aaGGgGgT
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2511 3.00e+03 TttGtATcCc.CAaTgaa
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2708 4.10e-16 cAcCaATaTtAaCAAGgaGATCAG
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2709 3.80e-14 TGTGaTATATTgAGTTCgCCAAAA
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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 GSU2330

Warning: No Functional annotations were found!

Module neighborhood information for GSU2330

GSU2330 has total of 34 gene neighbors in modules 175, 274
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0044 GSU0044 salmonella virulence plasmid 65kDa B protein /YD repeat protein (NCBI) 274, 300
GSU0251 GSU0251 hypothetical protein (VIMSS) 124, 274
GSU0300 GSU0300 sigma-54 dependent DNA-binding response regulator, interruption-N (VIMSS) 124, 274
GSU0381 GSU0381 lipoprotein, putative (VIMSS) 274, 296
GSU0673 GSU0673 hypothetical protein (NCBI) 175, 211
GSU0718 GSU0718 sensory box histidine kinase/response regulator (VIMSS) 175, 211
GSU0885 GSU0885 cobyrinic acid a,c-diamide synthase family protein (NCBI) 224, 274
GSU0907 GSU0907 thiF family protein (NCBI) 175, 339
GSU1051 GSU1051 hypothetical protein (VIMSS) 274, 291
GSU1539 xth exodeoxyribonuclease III (NCBI) 274, 300
GSU1852 GSU1852 membrane protein, putative (VIMSS) 17, 274
GSU2119 GSU2119 integrative genetic element Gsu56, integrase (VIMSS) 70, 274
GSU2120 ihfA-2 integration host factor, alpha subunit (NCBI) 70, 274
GSU2141 GSU2141 ISGsu1, transposase, interruption (VIMSS) 124, 274
GSU2173 GSU2173 lipoprotein, putative (VIMSS) 79, 274
GSU2180 GSU2180 ISGsu1, transposase (VIMSS) 124, 274
GSU2181 GSU2181 hypothetical protein (VIMSS) 124, 274
GSU2182 GSU2182 hypothetical protein (VIMSS) 124, 274
GSU2321 GSU2321 hypothetical protein (VIMSS) 175, 311
GSU2323 GSU2323 membrane protein, putative (VIMSS) 175, 310
GSU2324 GSU2324 hypothetical protein (VIMSS) 27, 175
GSU2327 GSU2327 conserved hypothetical protein (VIMSS) 175, 244
GSU2329 cfa cyclopropane-fatty-acyl-phospholipid synthase (NCBI) 175, 244
GSU2330 GSU2330 membrane protein, putative (VIMSS) 175, 274
GSU2438 GSU2438 prevent-host-death family protein (NCBI) 269, 274
GSU2705 moaB molybdenum cofactor biosynthesis protein B (NCBI) 175, 224
GSU2825 GSU2825 membrane protein, putative (VIMSS) 175, 211
GSU2872 GSU2872 electron transfer flavoprotein, Etf beta-subunit/FixA family (VIMSS) 175, 320
GSU2873 GSU2873 radical SAM domain protein (NCBI) 175, 211
GSU3216 GSU3216 sensor histidine kinase, putative (VIMSS) 73, 175
GSU3245 GSU3245 DNA polymerase II, putative (NCBI) 73, 175
GSU3290 GSU3290 conserved hypothetical protein (VIMSS) 175, 320
GSU3418 GSU3418 sigma-54 dependent DNA-binding response regulator (VIMSS) 21, 274
GSU3419 GSU3419 sensor histidine kinase (VIMSS) 14, 274
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 GSU2330
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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