Organism : Geobacter sulfurreducens | Module List :
GSU3106

conserved hypothetical protein (NCBI)

CircVis
Functional Annotations (7)
Function System
Predicted alternative thymidylate synthase cog/ cog
dTMP biosynthetic process go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
thymidylate synthase (FAD) activity go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
thyX tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3106
(Mouseover regulator name to see its description)

GSU3106 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU3106 (19)
Regulator Module Operator
GSU0187 258 tf
GSU0266 258 tf
GSU0473 258 tf
GSU1320 258 tf
GSU1831 258 tf
GSU2915 258 tf
GSU3324 258 tf
GSU3396 258 tf
GSU0063 128 tf
GSU0147 128 tf
GSU0205 128 tf
GSU0836 128 tf
GSU1495 128 tf
GSU1831 128 tf
GSU1934 128 tf
GSU2033 128 tf
GSU2113 128 tf
GSU3324 128 tf
GSU3396 128 tf

Warning: GSU3106 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
2416 6.10e+02 CCGcaAcggcc
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2417 1.10e+03 CtgaCttcAcGgaTA
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2676 2.10e+02 AaTtAaaaCtaTtTT
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2677 3.00e+03 ccgcctcg.Caggcc.TTgac
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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 GSU3106

GSU3106 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Predicted alternative thymidylate synthase cog/ cog
dTMP biosynthetic process go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
thymidylate synthase (FAD) activity go/ molecular_function
Pyrimidine metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
thyX tigr/ tigrfam
Module neighborhood information for GSU3106

GSU3106 has total of 41 gene neighbors in modules 128, 258
Gene neighbors (41)
Gene Common Name Description Module membership
GSU0024 GSU0024 OmpA domain protein (VIMSS) 228, 258
GSU0153 argG argininosuccinate synthase (NCBI) 160, 258
GSU0224 GSU0224 conserved hypothetical protein (VIMSS) 40, 258
GSU0243 GSU0243 conserved hypothetical protein (VIMSS) 119, 128
GSU0317 GSU0317 conserved hypothetical protein (VIMSS) 60, 258
GSU0680 GSU0680 conserved hypothetical protein (VIMSS) 127, 128
GSU0850 GSU0850 hypothetical protein (NCBI) 258, 289
GSU0905 GSU0905 hypothetical protein (NCBI) 128, 225
GSU0969 ctpA-1 carboxy-terminal processing protease (NCBI) 3, 128
GSU0981 GSU0981 conserved hypothetical protein (VIMSS) 48, 258
GSU0988 GSU0988 conserved hypothetical protein (VIMSS) 48, 258
GSU1045 GSU1045 membrane protein, putative (NCBI) 128, 225
GSU1316 GSU1316 response regulator (VIMSS) 160, 258
GSU1610 GSU1610 efflux transporter, RND family, MFP subunit (NCBI) 113, 258
GSU1766 xseB exodeoxyribonuclease VII, small subunit (NCBI) 113, 258
GSU1867 GSU1867 hypothetical protein (VIMSS) 258, 264
GSU2294 GSU2294 cytochrome c family protein (NCBI) 250, 258
GSU2434 lipB lipoate-protein ligase B (NCBI) 40, 128
GSU2451 GSU2451 PilB-related protein (VIMSS) 40, 258
GSU2458 GSU2458 penicillin-binding protein, putative (NCBI) 160, 258
GSU2489 GSU2489 deoxyribonuclease, TatD family (VIMSS) 128, 160
GSU2496 GSU2496 hypothetical protein (VIMSS) 91, 258
GSU2514 GSU2514 hypothetical protein (VIMSS) 128, 140
GSU2585 GSU2585 hypothetical protein (VIMSS) 123, 128
GSU2603 rpsA ribosomal protein S1 (NCBI) 258, 262
GSU2652 GSU2652 methyl-accepting chemotaxis protein (VIMSS) 128, 275
GSU2655 pdhB pyruvate dehydrogenase complex E1 component, beta subunit (NCBI) 240, 258
GSU2721 hoxF NAD-reducing hydrogenase, alpha subunit (NCBI) 40, 128
GSU2722 GSU2722 NAD-reducing hydrogenase, putative (VIMSS) 112, 128
GSU2788 GSU2788 conserved hypothetical protein (NCBI) 128, 326
GSU2969 pleD sensory box/GGDEF family protein (NCBI) 26, 258
GSU3086 GSU3086 conserved hypothetical protein (VIMSS) 53, 258
GSU3106 GSU3106 conserved hypothetical protein (NCBI) 128, 258
GSU3112 GSU3112 cell division protein FtsK, putative (VIMSS) 128, 160
GSU3113 GSU3113 metallo-beta-lactamase family protein (VIMSS) 112, 128
GSU3137 GSU3137 cytochrome c family protein (NCBI) 40, 128
GSU3158 cysM cysteine synthase b (VIMSS) 140, 258
GSU3194 thiL thiamine monophosphate kinase (NCBI) 128, 326
GSU3235 rpmA ribosomal protein L27 (NCBI) 58, 258
GSU3294 GSU3294 rubredoxin-oxygen oxidoreductase, putative (VIMSS) 11, 258
GSU3349 GSU3349 cyclase, putative (NCBI) 128, 225
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 GSU3106
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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