Organism : Geobacter sulfurreducens | Module List :
GSU3407

membrane protein, putative (VIMSS)

CircVis
Functional Annotations (1)
Function System
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3407
(Mouseover regulator name to see its description)

GSU3407 is regulated by 22 influences and regulates 0 modules.
Regulators for GSU3407 (22)
Regulator Module Operator
GSU0205 103 tf
GSU0280 103 tf
GSU0721 103 tf
GSU1268 103 tf
GSU1277 103 tf
GSU1653 103 tf
GSU2041 103 tf
GSU2202 103 tf
GSU2670 103 tf
GSU2741 103 tf
GSU2779 103 tf
GSU3396 103 tf
GSU3418 103 tf
GSU3457 103 tf
GSU0079 18 tf
GSU0207 18 tf
GSU1250 18 tf
GSU1626 18 tf
GSU1727 18 tf
GSU1905 18 tf
GSU2524 18 tf
GSU2831 18 tf

Warning: GSU3407 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
2196 3.70e-02 tacTtTtttcAttttT
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2197 9.70e-04 AtGtcAatgcCtTTttGccg
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2366 2.10e+02 AaaCattaaAattGctcacat
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2367 1.20e+02 GaacATttTcaaagAaAa.cAA
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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 GSU3407

GSU3407 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
membrane go/ cellular_component
Module neighborhood information for GSU3407

GSU3407 has total of 48 gene neighbors in modules 18, 103
Gene neighbors (48)
Gene Common Name Description Module membership
GSU0079 GSU0079 transcriptional regulator, Cro/CI family (VIMSS) 3, 18
GSU0110 atpH ATP synthase F1, delta subunit (NCBI) 18, 243
GSU0161 GSU0161 hypothetical protein (VIMSS) 18, 19
GSU0207 GSU0207 cold-shock domain family protein (VIMSS) 18, 116
GSU0312 GSU0312 hypothetical protein (VIMSS) 18, 243
GSU0338 nuoA-1 NADH dehydrogenase I, A subunit (NCBI) 18, 243
GSU0384 GSU0384 conserved hypothetical protein (VIMSS) 18, 243
GSU0390 GSU0390 conserved hypothetical protein (VIMSS) 11, 18
GSU0507 GSU0507 membrane protein, putative (NCBI) 18, 238
GSU0592 GSU0592 cytochrome c family protein (NCBI) 18, 116
GSU0660 ispE 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI) 18, 228
GSU0693 GSU0693 sensory box histidine kinase (VIMSS) 103, 157
GSU0765 GSU0765 hypothetical protein (VIMSS) 103, 321
GSU0959 GSU0959 hypothetical protein (VIMSS) 103, 179
GSU0962 GSU0962 sensor histidine kinase (VIMSS) 18, 42
GSU1264 GSU1264 conserved domain protein (VIMSS) 103, 105
GSU1265 GSU1265 sensor histidine kinase/response regulator (VIMSS) 103, 105
GSU1336 GSU1336 membrane protein, TerC family (NCBI) 18, 207
GSU1386 GSU1386 conserved hypothetical protein (VIMSS) 18, 315
GSU1444 GSU1444 conserved hypothetical protein (VIMSS) 103, 295
GSU1500 GSU1500 hypothetical protein (VIMSS) 103, 105
GSU1501 GSU1501 ABC transporter, ATP-binding protein (VIMSS) 103, 303
GSU1502 GSU1502 prenyltransferase, UbiA family (VIMSS) 103, 105
GSU1503 GSU1503 glycosyl transferase, group 2 family protein (VIMSS) 103, 315
GSU1504 GSU1504 ABC transporter, permease protein, ABC-2 family (VIMSS) 103, 105
GSU1505 GSU1505 ABC transporter, ATP-binding protein (VIMSS) 103, 105
GSU1712 GSU1712 hypothetical protein (VIMSS) 18, 42
GSU1781 GSU1781 hypothetical protein (VIMSS) 17, 18
GSU1784 GSU1784 type IV pilus biogenesis protein PilC, putative (VIMSS) 17, 18
GSU1873 pepF oligoendopeptidase F (NCBI) 103, 191
GSU2643 GSU2643 cytochrome c family protein (NCBI) 18, 136
GSU2748 GSU2748 cytochrome c family protein, putative (NCBI) 103, 130
GSU2943 GSU2943 hypothetical protein (VIMSS) 103, 105
GSU2948 GSU2948 membrane protein, putative (NCBI) 103, 178
GSU2949 GSU2949 PAP2 family protein (VIMSS) 103, 146
GSU2950 GSU2950 ABC transporter, permease protein (VIMSS) 103, 130
GSU3165 GSU3165 conserved domain protein (NCBI) 103, 132
GSU3170 GSU3170 hypothetical protein (VIMSS) 103, 303
GSU3171 GSU3171 conserved domain protein (NCBI) 51, 103
GSU3172 GSU3172 conserved hypothetical protein (VIMSS) 103, 303
GSU3173 GSU3173 conserved hypothetical protein (VIMSS) 103, 327
GSU3175 GSU3175 hypothetical protein (VIMSS) 103, 303
GSU3177 GSU3177 Rhs family protein (NCBI) 103, 105
GSU3185 GSU3185 hypothetical protein (VIMSS) 103, 105
GSU3206 dksA dnaK suppressor protein, putative (NCBI) 18, 35
GSU3404 GSU3404 amino acid ABC transporter, ATP-binding protein (VIMSS) 103, 117
GSU3405 GSU3405 amino acid ABC transporter, permease protein (VIMSS) 11, 18
GSU3407 GSU3407 membrane protein, putative (VIMSS) 18, 103
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 GSU3407
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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