Organism : Geobacter sulfurreducens | Module List :
GSU2540

transcriptional regulator, Cro/CI family (VIMSS)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2540
(Mouseover regulator name to see its description)

GSU2540 is regulated by 14 influences and regulates 3 modules.
Regulators for GSU2540 (14)
Regulator Module Operator
GSU0372 304 tf
GSU1115 304 tf
GSU2354 304 tf
GSU2787 304 tf
GSU2831 304 tf
GSU2868 304 tf
GSU2915 304 tf
GSU3387 304 tf
GSU0372 181 tf
GSU1039 181 tf
GSU1495 181 tf
GSU2177 181 tf
GSU2520 181 tf
GSU2523 181 tf

Warning: GSU2540 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
2522 5.90e-02 gcgTtctTaaAAg.agttta
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2523 2.70e+02 tTcTCTTTGacttAcataaaa
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2766 1.40e-02 Ttc.gTAgGA.aaAgTaTgCtA
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2767 1.10e+02 A.gaTttcTcaagtccggCaAaaA
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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 GSU2540

GSU2540 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for GSU2540

GSU2540 has total of 60 gene neighbors in modules 181, 304
Gene neighbors (60)
Gene Common Name Description Module membership
GSU0105 GSU0105 cytochrome c family protein, putative (NCBI) 180, 181
GSU0107 spo0J parB-like domain protein (NCBI) 147, 181
GSU0217 noxC nitroreductase family protein (NCBI) 110, 304
GSU0277 GSU0277 ABC transporter, ATP-binding/permease protein (VIMSS) 104, 304
GSU0294 GSU0294 HD domain protein (NCBI) 220, 304
GSU0372 GSU0372 sigma-54 dependent DNA-binding response regulator (VIMSS) 224, 304
GSU0374 hypA hydrogenase expression/formation protein hupa (NCBI) 283, 304
GSU0375 gcvT glycine cleavage system T protein (NCBI) 296, 304
GSU0422 fliN flagellar motor switch protein FliN (NCBI) 181, 234
GSU0515 GSU0515 universal stress protein family (VIMSS) 69, 181
GSU0698 GSU0698 PBS lyase HEAT-like repeat protein (NCBI) 296, 304
GSU0758 GSU0758 membrane protein, putative (VIMSS) 181, 278
GSU0899 GSU0899 conserved hypothetical protein (VIMSS) 69, 304
GSU0935 GSU0935 methyl-accepting chemotaxis protein, putative (VIMSS) 155, 304
GSU0943 GSU0943 hypothetical protein (VIMSS) 304, 335
GSU1039 GSU1039 sigma-54 dependent DNA-binding response regulator (VIMSS) 181, 269
GSU1047 GSU1047 conserved hypothetical protein (VIMSS) 181, 253
GSU1114 GSU1114 TPR domain protein (VIMSS) 181, 267
GSU1169 GSU1169 hypothetical protein (VIMSS) 165, 304
GSU1181 GSU1181 hypothetical protein (VIMSS) 176, 181
GSU1216 cydC transport ATP-binding protein CydC (NCBI) 8, 181
GSU1222 GSU1222 histone deacetylase/AcuC/AphA family protein (VIMSS) 106, 181
GSU1240 GSU1240 hypothetical protein (VIMSS) 176, 181
GSU1281 nikO component of nickel ABC transport system (Dmitry Rodionov) 181, 278
GSU1310 GSU1310 pyridine nucleotide-disulfide oxidoreductase (Regina ONeil) 181, 205
GSU1315 merA-1 mercuric reductase (NCBI) 296, 304
GSU1319 GSU1319 sensor histidine kinase (VIMSS) 106, 181
GSU1372 GSU1372 3-hydroxyisobutyrate dehydrogenase family protein (VIMSS) 59, 304
GSU1446 GSU1446 radical SAM domain protein (NCBI) 181, 207
GSU1545 GSU1545 transporter, LysE family (VIMSS) 181, 338
GSU1550 GSU1550 4-oxalocrotonate tautomerase family protein (VIMSS) 220, 304
GSU1573 GSU1573 CAAX amino terminal protease family protein (NCBI) 181, 253
GSU1619 cheY-4 chemotaxis protein CheY (NCBI) 59, 304
GSU1713 GSU1713 conserved hyothetical protein, truncation (VIMSS) 70, 304
GSU1715 GSU1715 hypothetical protein (VIMSS) 51, 181
GSU1740 GSU1740 cytochrome c family protein, putative (VIMSS) 69, 181
GSU2116 GSU2116 hypothetical protein (VIMSS) 181, 253
GSU2117 GSU2117 hypothetical protein (VIMSS) 181, 278
GSU2163 GSU2163 hypothetical protein (VIMSS) 181, 278
GSU2177 GSU2177 hypothetical protein (VIMSS) 113, 181
GSU2293 GSU2293 hypothetical protein (VIMSS) 181, 338
GSU2297 GSU2297 sensory box histidine kinase (VIMSS) 71, 181
GSU2312 GSU2312 sulfate transporter family protein (VIMSS) 130, 181
GSU2472 vapC virulence associated protein C (NCBI) 181, 193
GSU2474 GSU2474 hypothetical protein (VIMSS) 88, 181
GSU2538 nspC carboxynorspermidine decarboxylase (NCBI) 15, 304
GSU2539 LYS1 saccharopine dehydrogenase (NCBI) 25, 304
GSU2540 GSU2540 transcriptional regulator, Cro/CI family (VIMSS) 181, 304
GSU2541 proC pyrroline-5-carboxylate reductase (NCBI) 114, 304
GSU2577 GSU2577 hypothetical protein (VIMSS) 296, 304
GSU2646 GSU2646 hypothetical protein (VIMSS) 79, 304
GSU2664 GSU2664 outer membrane efflux protein (VIMSS) 181, 244
GSU2671 GSU2671 hypothetical protein (VIMSS) 82, 304
GSU2744 GSU2744 major facilitator family transporter (VIMSS) 49, 304
GSU2745 GSU2745 ATPase, AAA family (VIMSS) 49, 304
GSU2746 GSU2746 conserved domain protein (NCBI) 269, 304
GSU2927 GSU2927 cytochrome c, putative (NCBI) 181, 327
GSU3155 GSU3155 cytochrome c nitrite reductase, small subunit NrfH, putative (VIMSS) 78, 304
GSU3184 GSU3184 hypothetical protein (VIMSS) 181, 300
GSU3361 GSU3361 transglutaminase domain protein (NCBI) 180, 181
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 GSU2540
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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