Organism : Geobacter sulfurreducens | Module List :
GSU2724

cytochrome c family protein (NCBI)

CircVis
Functional Annotations (5)
Function System
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
GSu_C4xC__C2xCH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2724
(Mouseover regulator name to see its description)

GSU2724 is regulated by 22 influences and regulates 0 modules.
Regulators for GSU2724 (22)
Regulator Module Operator
GSU0187 23 tf
GSU0359 23 tf
GSU0625 23 tf
GSU1013 23 tf
GSU1277 23 tf
GSU1653 23 tf
GSU1934 23 tf
GSU2506 23 tf
GSU2523 23 tf
GSU2571 23 tf
GSU2753 23 tf
GSU2941 23 tf
GSU3109 23 tf
GSU3363 23 tf
GSU0175 237 tf
GSU0187 237 tf
GSU0581 237 tf
GSU1003 237 tf
GSU1934 237 tf
GSU2033 237 tf
GSU2753 237 tf
GSU3206 237 tf

Warning: GSU2724 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
2206 2.70e+03 ACgGg.aTcgCcG
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2207 2.80e+03 aaAgATTG.AT
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2634 5.70e+01 cggGcCGgTaTtTTC
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2635 4.00e+02 cGC.GgggCGg
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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 GSU2724

GSU2724 is enriched for 5 functions in 4 categories.
Enrichment Table (5)
Function System
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
GSu_C4xC__C2xCH tigr/ tigrfam
Module neighborhood information for GSU2724

GSU2724 has total of 36 gene neighbors in modules 23, 237
Gene neighbors (36)
Gene Common Name Description Module membership
GSU0084 GSU0084 aminotransferase, classes I and II (NCBI) 3, 237
GSU0187 GSU0187 conserved hypothetical protein (VIMSS) 237, 240
GSU0219 GSU0219 cytochrome c oxidase, subunit I (VIMSS) 49, 237
GSU0221 GSU0221 cytochrome c oxidase, subunit IV (VIMSS) 49, 237
GSU0601 GSU0601 alpha amylase family protein (VIMSS) 23, 275
GSU0909 GSU0909 pyridine nucleotide-disulphide oxidoreductase family protein (NCBI) 138, 237
GSU2034 GSU2034 hypothetical protein (VIMSS) 23, 138
GSU2036 GSU2036 hypothetical protein (VIMSS) 23, 138
GSU2037 GSU2037 hypothetical protein (VIMSS) 23, 138
GSU2038 GSU2038 hypothetical protein (NCBI) 23, 138
GSU2039 GSU2039 hypothetical protein (VIMSS) 23, 138
GSU2351 GSU2351 cation-transport ATPase, E1-E2 family (VIMSS) 49, 237
GSU2430 GSU2430 SPFH/Band 7 domain protein (VIMSS) 23, 256
GSU2436 GSU2436 dehydrogenase complex, E1 component, beta subunit (NCBI) 182, 237
GSU2449 sucA 2-oxoglutarate dehydrogenase, E1 component (NCBI) 182, 237
GSU2584 GSU2584 lipoprotein, putative (VIMSS) 138, 237
GSU2633 GSU2633 lipoprotein, putative (VIMSS) 23, 311
GSU2649 GSU2649 amino acid ABC transporter, amino acid-binding protein (VIMSS) 237, 240
GSU2650 GSU2650 amino acid ABC transporter, permease protein, putative (VIMSS) 49, 237
GSU2702 GSU2702 ABC transporter, ATP-binding protein (VIMSS) 23, 256
GSU2703 moeA molybdopterin biosynthesis protein MoeA (NCBI) 23, 256
GSU2704 moaC molybdenum cofactor biosynthesis protein MoaC (NCBI) 23, 256
GSU2724 GSU2724 cytochrome c family protein (NCBI) 23, 237
GSU2725 GSU2725 cytochrome c family protein (VIMSS) 23, 237
GSU2726 GSU2726 hypothetical protein (VIMSS) 133, 237
GSU2882 GSU2882 cytochrome c family protein (VIMSS) 23, 256
GSU3051 flgG-1 flagellar basal-body rod protein FlgG (NCBI) 23, 138
GSU3331 pyk pyruvate kinase (NCBI) 237, 256
GSU3352 GSU3352 hypothetical protein (VIMSS) 237, 240
GSU3388 GSU3388 membrane protein, putative (VIMSS) 23, 311
GSU3430 nuoM-2 NADH dehydrogenase I, M subunit (NCBI) 23, 256
GSU3432 nuoI NADH dehydrogenase I, K subunit (NCBI) 23, 256
GSU3436 nuoH-2 NADH dehydrogenase I, H subunit (NCBI) 23, 256
GSU3443 nuoE-2 NADH dehydrogenase I, E subunit (NCBI) 23, 256
GSU3444 nuoBCD NADH dehydrogenase I, B/C/D subunits (VIMSS) 23, 167
GSU3448 ackA-2 acetate kinase (NCBI) 23, 237
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 GSU2724
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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