Organism : Geobacter sulfurreducens | Module List :
GSU0063

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulator cog/ cog
nucleotide binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0063
(Mouseover regulator name to see its description)

GSU0063 is regulated by 17 influences and regulates 11 modules.
Regulators for GSU0063 (17)
Regulator Module Operator
GSU0063 79 tf
GSU1115 79 tf
GSU1250 79 tf
GSU1992 79 tf
GSU2041 79 tf
GSU2809 79 tf
GSU2868 79 tf
GSU2915 79 tf
GSU3217 79 tf
GSU0063 141 tf
GSU1039 141 tf
GSU1072 141 tf
GSU1250 141 tf
GSU1483 141 tf
GSU1569 141 tf
GSU1617 141 tf
GSU3053 141 tf

Warning: GSU0063 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
2318 4.90e+01 AAGAAt.tt.C.gttatgccgAaa
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2319 2.00e+04 GCtGgCGCaGatGGGCgTc
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2442 4.50e-01 AAAAtGgtactTtTtAtCcTAaAA
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2443 8.30e-01 ac.AtcCTCtttTcctggtgGgaA
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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 GSU0063

GSU0063 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator cog/ cog
nucleotide binding go/ molecular_function
Module neighborhood information for GSU0063

GSU0063 has total of 52 gene neighbors in modules 79, 141
Gene neighbors (52)
Gene Common Name Description Module membership
GSU0063 GSU0063 conserved hypothetical protein (VIMSS) 79, 141
GSU0120 GSU0120 hydrogenase maturation protease (VIMSS) 82, 141
GSU0225 GSU0225 hypothetical protein (VIMSS) 79, 84
GSU0264 GSU0264 drug resistance transporter, Bcr/CflA family (VIMSS) 82, 141
GSU0275 GSU0275 hypothetical protein (VIMSS) 82, 141
GSU0278 GSU0278 outer membrane efflux protein (VIMSS) 82, 141
GSU0314 GSU0314 general secretion protein E N-terminal domain protein (NCBI) 79, 278
GSU0425 fliR flagellar biosynthesis protein FliR (NCBI) 82, 141
GSU0435 GSU0435 MSHA biogenesis protein MshE, putative (VIMSS) 79, 272
GSU0683 GSU0683 methyl-accepting chemotaxis protein, putative (VIMSS) 45, 79
GSU0691 GSU0691 translation initation factor SUI1, putative (NCBI) 71, 79
GSU0701 GSU0701 cytochrome c family protein (NCBI) 79, 206
GSU0820 sppA-1 signal peptide peptidase SppA, 36K type (NCBI) 36, 79
GSU0822 GSU0822 sensory box histidine kinase (VIMSS) 6, 141
GSU0900 GSU0900 hypothetical protein (VIMSS) 79, 272
GSU1097 pstA phosphate ABC transporter, permease protein (NCBI) 82, 141
GSU1302 GSU1302 sensor histidine kinase/response regulator (VIMSS) 79, 180
GSU1327 GSU1327 homocysteine S-methyltransferase domain protein (VIMSS) 79, 260
GSU1418 GSU1418 hypothetical protein (VIMSS) 78, 79
GSU1570 GSU1570 membrane protein, TerC family (NCBI) 15, 79
GSU1572 GSU1572 ribD domain protein (NCBI) 51, 79
GSU1751 GSU1751 hypothetical protein (VIMSS) 59, 141
GSU1752 efp-2 translation elongation factor P (NCBI) 56, 141
GSU2095 GSU2095 NADH oxidase, putative (VIMSS) 1, 79
GSU2173 GSU2173 lipoprotein, putative (VIMSS) 79, 274
GSU2289 GSU2289 nicotinate phosphoribosyltransferase, putative (NCBI) 46, 79
GSU2295 GSU2295 hypothetical protein (VIMSS) 141, 278
GSU2296 GSU2296 HD domain protein (VIMSS) 141, 266
GSU2299 GSU2299 cytochrome c family protein (NCBI) 82, 141
GSU2358 GSU2358 isoamylase family protein (VIMSS) 79, 142
GSU2360 GSU2360 maltooligosyltrehalose synthase, putative (VIMSS) 63, 79
GSU2369 GSU2369 hypothetical protein (VIMSS) 59, 79
GSU2384 GSU2384 sensor histidine kinase (VIMSS) 79, 269
GSU2401 GSU2401 sensory box histidine kinase/response regulator (VIMSS) 82, 141
GSU2416 cheW-8 chemotaxis protein CheW (NCBI) 59, 79
GSU2453 GSU2453 membrane protein, putative (VIMSS) 51, 79
GSU2502 GSU2502 spermine/spermidine synthase family protein (VIMSS) 141, 341
GSU2510 GSU2510 hypothetical protein (VIMSS) 9, 79
GSU2530 GSU2530 GTPase YjeQ (NCBI) 45, 141
GSU2531 GSU2531 sensory box histidine kinase (VIMSS) 79, 82
GSU2575 GSU2575 sensor histidine kinase/response regulator (VIMSS) 40, 141
GSU2578 cheW-9 purine-binding chemotaxis protein CheW (NCBI) 79, 300
GSU2579 GSU2579 methyl-accepting chemotaxis protein (VIMSS) 36, 141
GSU2580 GSU2580 hypothetical protein (VIMSS) 82, 141
GSU2582 GSU2582 hypothetical protein (VIMSS) 79, 151
GSU2646 GSU2646 hypothetical protein (VIMSS) 79, 304
GSU2684 GSU2684 hypothetical protein (VIMSS) 141, 159
GSU2790 GSU2790 hypothetical protein (VIMSS) 65, 141
GSU2931 GSU2931 hypothetical protein (VIMSS) 70, 79
GSU3030 GSU3030 hypothetical protein (VIMSS) 6, 141
GSU3047 flgI flagellar P-ring protein FlgI (NCBI) 141, 186
GSU3227 GSU3227 hypothetical protein (VIMSS) 82, 141
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 GSU0063
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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