Organism : Geobacter sulfurreducens | Module List :
GSU3218

cytochrome c family protein (NCBI)

CircVis
Functional Annotations (3)
Function System
electron transport go/ biological_process
heme binding go/ molecular_function
paired_CXXCH_1 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3218
(Mouseover regulator name to see its description)

GSU3218 is regulated by 16 influences and regulates 0 modules.
Regulators for GSU3218 (16)
Regulator Module Operator
GSU0254 135 tf
GSU0551 135 tf
GSU0735 135 tf
GSU1072 135 tf
GSU2716 135 tf
GSU3108 135 tf
GSU3217 135 tf
GSU0175 155 tf
GSU0300 155 tf
GSU0951 155 tf
GSU1586 155 tf
GSU1940 155 tf
GSU2354 155 tf
GSU2868 155 tf
GSU3108 155 tf
GSU3217 155 tf

Warning: GSU3218 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
2430 9.40e-05 TtttgaaaAatagtt.TAAaGT.T
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2431 2.40e+02 gTcaAtaAAaatAaAACAcc.ttT
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2470 2.80e+00 AAgCAaccaaTgcATTATTcc
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2471 6.60e+03 AcatAtTgTTtacggTGGaaA
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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 GSU3218

GSU3218 is enriched for 3 functions in 4 categories.
Enrichment Table (3)
Function System
electron transport go/ biological_process
heme binding go/ molecular_function
paired_CXXCH_1 tigr/ tigrfam
Module neighborhood information for GSU3218

GSU3218 has total of 42 gene neighbors in modules 135, 155
Gene neighbors (42)
Gene Common Name Description Module membership
GSU0132 GSU0132 conserved hypothetical protein (VIMSS) 155, 157
GSU0268 GSU0268 membrane protein, putative (VIMSS) 137, 155
GSU0429 GSU0429 conserved hypothetical protein (VIMSS) 135, 275
GSU0576 GSU0576 conserved domain protein (VIMSS) 155, 314
GSU0754 GSU0754 fibronectin type III domain protein (VIMSS) 155, 269
GSU0755 GSU0755 hypothetical protein (VIMSS) 155, 269
GSU0830 GSU0830 heavy metal efflux pump, CzcA family (VIMSS) 27, 155
GSU0837 GSU0837 response regulator (VIMSS) 21, 155
GSU0838 GSU0838 hypothetical protein (VIMSS) 155, 236
GSU0839 GSU0839 hypothetical protein (VIMSS) 155, 208
GSU0935 GSU0935 methyl-accepting chemotaxis protein, putative (VIMSS) 155, 304
GSU1022 GSU1022 hypothetical protein (VIMSS) 93, 155
GSU1041 GSU1041 methyl-accepting chemotaxis protein (VIMSS) 155, 206
GSU1072 GSU1072 transcriptional regulator, IclR family (VIMSS) 57, 135
GSU1304 GSU1304 methyl-accepting chemotaxis protein (VIMSS) 82, 155
GSU1858 GSU1858 IPT/TIG domain protein (VIMSS) 155, 236
GSU2005 GSU2005 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI) 135, 142
GSU2006 GSU2006 branched-chain amino acid ABC transporter, permease protein (NCBI) 135, 142
GSU2007 GSU2007 branched-chain amino acid ABC transporter, permease protein (NCBI) 135, 142
GSU2008 GSU2008 branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 135, 142
GSU2009 GSU2009 branched-chain amino acid ABC transporter, ATP-binding protein (VIMSS) 135, 142
GSU2010 GSU2010 CBS domain protein (VIMSS) 135, 142
GSU2136 GSU2136 heavy metal efflux pump, CzcB family (VIMSS) 113, 155
GSU2155 GSU2155 hypothetical protein (VIMSS) 70, 135
GSU2164 GSU2164 hypothetical protein (VIMSS) 78, 155
GSU2314 GSU2314 sensory box histidine kinase/response regulator (VIMSS) 155, 257
GSU2338 GSU2338 Na+/H+ antiporter component (VIMSS) 155, 171
GSU2355 GSU2355 hypothetical protein (VIMSS) 6, 135
GSU2388 GSU2388 sensory box histidine kinase (VIMSS) 82, 155
GSU2417 GSU2417 hypothetical protein (VIMSS) 57, 135
GSU2419 GSU2419 nickel-dependent hydrogenase, large subunit (VIMSS) 78, 135
GSU2557 GSU2557 polysaccharide deacetylase family protein (NCBI) 122, 135
GSU2598 GSU2598 hypothetical protein (VIMSS) 155, 179
GSU2630 GSU2630 serine/threonine protein phosphatase, putative (VIMSS) 155, 257
GSU2679 GSU2679 conserved hypothetical protein (VIMSS) 155, 180
GSU2768 GSU2768 hypothetical protein (VIMSS) 122, 135
GSU3016 GSU3016 hypothetical protein (VIMSS) 122, 135
GSU3120 GSU3120 conserved hypothetical protein (VIMSS) 122, 135
GSU3218 GSU3218 cytochrome c family protein (NCBI) 135, 155
GSU3225 GSU3225 NHL repeat domain protein (VIMSS) 16, 155
GSU3226 GSU3226 cytochrome c family protein (NCBI) 155, 337
GSU3355 GSU3355 hypothetical protein (VIMSS) 135, 246
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 GSU3218
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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