Organism : Geobacter sulfurreducens | Module List :
GSU3466

membrane protein, putative (VIMSS)

CircVis
Functional Annotations (6)
Function System
Preprotein translocase subunit YidC cog/ cog
integral to membrane go/ cellular_component
protein insertion into membrane go/ biological_process
Protein export kegg/ kegg pathway
Bacterial secretion system kegg/ kegg pathway
yidC_oxa1_cterm tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3466
(Mouseover regulator name to see its description)

GSU3466 is regulated by 12 influences and regulates 0 modules.
Regulators for GSU3466 (12)
Regulator Module Operator
GSU0018 230 tf
GSU1379 230 tf
GSU1483 230 tf
GSU2041 230 tf
GSU2237 230 tf
GSU3396 230 tf
GSU1639 315 tf
GSU1905 315 tf
GSU2041 315 tf
GSU2625 315 tf
GSU2831 315 tf
GSU3387 315 tf

Warning: GSU3466 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
2620 5.80e+02 aatagtaTactGTatAcacaa
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2621 2.40e+04 GGcAAaGggGc
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2786 6.00e+01 tTcAtaT.atT
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2787 4.00e+03 AaAaAAcAcAagTT
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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 GSU3466

GSU3466 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Preprotein translocase subunit YidC cog/ cog
integral to membrane go/ cellular_component
protein insertion into membrane go/ biological_process
Protein export kegg/ kegg pathway
Bacterial secretion system kegg/ kegg pathway
yidC_oxa1_cterm tigr/ tigrfam
Module neighborhood information for GSU3466

GSU3466 has total of 39 gene neighbors in modules 230, 315
Gene neighbors (39)
Gene Common Name Description Module membership
GSU0097 GSU0097 pyruvate ferredoxin/flavodoxin oxidoreductase (VIMSS) 30, 230
GSU0114 atpC ATP synthase F1, epsilon subunit (NCBI) 170, 230
GSU0164 GSU0164 conserved hypothetical protein (VIMSS) 113, 315
GSU0179 GSU0179 NADPH-dependent FMN reductase domain protein (NCBI) 202, 230
GSU0342 nuoE-1 NADH dehydrogenase I, E subunit (NCBI) 230, 243
GSU0344 GSU0344 NADH dehydrogenase I, G subunit, putative (NCBI) 230, 305
GSU0352 psaD thiol peroxidase (NCBI) 130, 315
GSU0353 GSU0353 membrane protein, putative (NCBI) 314, 315
GSU0391 GSU0391 Outer membrane efflux family protein (VIMSS) 216, 230
GSU0654 moeB thiF family protein (NCBI) 11, 315
GSU0657 GSU0657 hypothetical protein (VIMSS) 53, 315
GSU1108 GSU1108 aldehyde dehydrogenase family protein (NCBI) 230, 327
GSU1312 GSU1312 radical SAM domain protein, selenocysteine-containing (NCBI) 139, 230
GSU1386 GSU1386 conserved hypothetical protein (VIMSS) 18, 315
GSU1483 GSU1483 transcriptional regulator, MarR family (VIMSS) 137, 230
GSU1503 GSU1503 glycosyl transferase, group 2 family protein (VIMSS) 103, 315
GSU1584 bioB biotin synthetase (Dmitry Rodionov) 120, 315
GSU1631 GSU1631 metallo-beta-lactamase family protein (VIMSS) 81, 315
GSU1639 GSU1639 Rrf2 family protein (NCBI) 264, 315
GSU1640 cydA cytochrome d ubiquinol oxidase, subunit I (NCBI) 264, 315
GSU1641 cydB cytochrome d ubiquinol oxidase, subunit II (NCBI) 264, 315
GSU1906 leuA 2-isopropylmalate synthase (NCBI) 137, 315
GSU1918 frr ribosome recycling factor (NCBI) 230, 248
GSU1999 hfq hfq protein (NCBI) 42, 315
GSU2014 GSU2014 hypothetical protein (VIMSS) 108, 315
GSU2553 GSU2553 glycosyl transferase, group 2 family protein (VIMSS) 231, 315
GSU2634 GSU2634 hypothetical protein (VIMSS) 195, 230
GSU2637 GSU2637 alcohol dehydrogenase, zinc-containing (VIMSS) 129, 230
GSU2844 rpsN ribosomal protein S14 (NCBI) 315, 340
GSU3037 fliD flagellar hook-associated protein 2 (NCBI) 150, 230
GSU3063 ftsZ cell division protein FtsZ (NCBI) 230, 264
GSU3098 hisB imidazoleglycerol-phosphate dehydratase (NCBI) 203, 315
GSU3123 GSU3123 aldehyde ferredoxin oxidoreductase domain protein (VIMSS) 137, 230
GSU3125 GSU3125 alcohol dehydrogenase, zinc-containing (VIMSS) 137, 230
GSU3246 GSU3246 thioredoxin peroxidase (VIMSS) 264, 315
GSU3293 GSU3293 conserved hypothetical protein (VIMSS) 35, 315
GSU3300 GSU3300 biotin-requiring enzyme subunit (NCBI) 230, 327
GSU3303 GSU3303 methylmalonyl-CoA epimerase (VIMSS) 106, 230
GSU3466 GSU3466 membrane protein, putative (VIMSS) 230, 315
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 GSU3466
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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