Organism : Geobacter sulfurreducens | Module List :
GSU2811 hsc

cytochrome c Hsc (NCBI)

CircVis
Functional Annotations (6)
Function System
Cytochrome c peroxidase cog/ cog
cytochrome-c peroxidase activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2811
(Mouseover regulator name to see its description)

GSU2811 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU2811 hsc (17)
Regulator Module Operator
GSU0147 195 tf
GSU0267 195 tf
GSU0736 195 tf
GSU1003 195 tf
GSU1013 195 tf
GSU1129 195 tf
GSU1525 195 tf
GSU1586 195 tf
GSU1687 195 tf
GSU2041 195 tf
GSU2741 195 tf
GSU2980 195 tf
GSU3421 195 tf
GSU1013 65 tf
GSU1831 65 tf
GSU2735 65 tf
GSU2753 65 tf

Warning: GSU2811 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
2290 1.10e-03 AcAAATtTtccAaAgtAACAT
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2291 9.20e+00 tcCgacag.cAagGgggtatcggC
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2550 3.50e-01 gtgatG.c.GcagcCGccgctgtC
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2551 8.50e+01 aAaAaAGGAggttgA
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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 GSU2811

GSU2811 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Cytochrome c peroxidase cog/ cog
cytochrome-c peroxidase activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
Module neighborhood information for GSU2811

GSU2811 has total of 44 gene neighbors in modules 65, 195
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0057 GSU0057 CRISPR-associated protein Cas1/Cas4 (NCBI) 157, 195
GSU0058 GSU0058 CRISPR-associated protein Cas2, putative (NCBI) 157, 195
GSU0185 GSU0185 membrane protein, putative (VIMSS) 165, 195
GSU0392 GSU0392 efflux transporter, RND family, MFP subunit (NCBI) 195, 251
GSU0712 GSU0712 hypothetical protein (VIMSS) 195, 288
GSU0713 GSU0713 hypothetical protein (VIMSS) 195, 288
GSU0715 GSU0715 hypothetical protein (VIMSS) 195, 288
GSU0716 GSU0716 hypothetical protein (NCBI) 65, 193
GSU0818 GSU0818 aldehyde dehydrogenase family protein (VIMSS) 65, 210
GSU0852 GSU0852 lipoprotein, putative (VIMSS) 16, 65
GSU0853 GSU0853 CBS domain protein (VIMSS) 65, 253
GSU0854 GSU0854 membrane protein (NCBI) 65, 164
GSU1171 GSU1171 conserved hypothetical protein (VIMSS) 195, 234
GSU1396 GSU1396 hypothetical protein (VIMSS) 65, 208
GSU1397 GSU1397 cytochrome c family protein, putative (NCBI) 65, 208
GSU1398 GSU1398 SCO1/SenC family protein (VIMSS) 65, 210
GSU1613 mutY A/G-specific adenine glycosylase, putative (NCBI) 25, 65
GSU1696 GSU1696 MoxR family protein (VIMSS) 65, 133
GSU1726 GSU1726 hypothetical protein (VIMSS) 195, 240
GSU1949 GSU1949 hypothetical protein (VIMSS) 65, 264
GSU1985 GSU1985 outer membrane protein, putative (VIMSS) 65, 247
GSU1987 GSU1987 TPR domain protein (VIMSS) 65, 247
GSU2100 katG catalase/peroxidase (NCBI) 65, 321
GSU2403 GSU2403 hypothetical protein (VIMSS) 65, 97
GSU2634 GSU2634 hypothetical protein (VIMSS) 195, 230
GSU2635 GSU2635 conserved hypothetical protein (NCBI) 195, 259
GSU2636 GSU2636 alpha-amylase family protein (VIMSS) 195, 252
GSU2682 GSU2682 conserved hypothetical protein (VIMSS) 49, 65
GSU2731 ferA polyheme membrane-associated cytochrome c (NCBI) 195, 214
GSU2732 GSU2732 cytochrome c family protein (NCBI) 195, 214
GSU2733 GSU2733 hypothetical protein (VIMSS) 195, 214
GSU2735 GSU2735 transcriptional regulator, TetR family (NCBI) 65, 66
GSU2737 GSU2737 polyheme membrane-associated cytochrome c (VIMSS) 195, 214
GSU2739 GSU2739 hypothetical protein (VIMSS) 195, 214
GSU2742 GSU2742 hypothetical protein (VIMSS) 65, 193
GSU2743 GSU2743 cytochrome c family protein (VIMSS) 65, 193
GSU2790 GSU2790 hypothetical protein (VIMSS) 65, 141
GSU2791 GSU2791 hypothetical protein (RefSeq) 65, 157
GSU2792 GSU2792 conserved hypothetical protein (NCBI) 65, 310
GSU2811 hsc cytochrome c Hsc (NCBI) 65, 195
GSU2812 GSU2812 glutaredoxin family protein (VIMSS) 134, 195
GSU2813 ccpA-2 cytochrome c551 peroxidase (NCBI) 65, 99
GSU2894 GSU2894 conserved hypothetical protein (VIMSS) 109, 195
GSU3188 GSU3188 rubredoxin (VIMSS) 42, 65
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 GSU2811
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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