Organism : Geobacter sulfurreducens | Module List :
GSU0280

transcriptional regulator, Fis family (VIMSS)

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0280
(Mouseover regulator name to see its description)

GSU0280 is regulated by 12 influences and regulates 25 modules.
Regulators for GSU0280 (12)
Regulator Module Operator
GSU0280 76 tf
GSU1293 76 tf
GSU1495 76 tf
GSU2033 76 tf
GSU2041 76 tf
GSU2952 76 tf
GSU3089 76 tf
GSU3324 76 tf
GSU0280 88 tf
GSU0598 88 tf
GSU2506 88 tf
GSU2670 88 tf

Warning: GSU0280 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
2312 2.20e-07 GAGACAGCCGGGatGCCGAAATaT
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2313 6.50e-07 CCGcGAGGaTGgggcgGAAAgCC
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2336 2.40e-02 aAAaCAagccgAgagcAtAG
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2337 1.50e-01 tcaATTTTtataAca
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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 GSU0280

GSU0280 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU0280

GSU0280 has total of 53 gene neighbors in modules 76, 88
Gene neighbors (53)
Gene Common Name Description Module membership
GSU0100 GSU0100 hypothetical protein (VIMSS) 88, 299
GSU0256 GSU0256 conserved hypothetical protein (NCBI) 88, 319
GSU0280 GSU0280 transcriptional regulator, Fis family (VIMSS) 76, 88
GSU0609 purH phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase (NCBI) 88, 231
GSU0622 GSU0622 membrane protein, putative (NCBI) 76, 232
GSU0702 GSU0702 cytochrome c family protein (VIMSS) 51, 76
GSU0816 GSU0816 ABC transporter, ATP-binding protein (VIMSS) 88, 158
GSU0877 GSU0877 response regulator (VIMSS) 51, 76
GSU1001 GSU1001 hypothetical protein (VIMSS) 76, 229
GSU1040 GSU1040 hypothetical protein (VIMSS) 36, 76
GSU1217 GSU1217 hypothetical protein (VIMSS) 88, 146
GSU1234 sppA-2 signal peptide peptidase SppA, 36K type (NCBI) 35, 88
GSU1247 GSU1247 hypothetical protein (VIMSS) 76, 292
GSU1293 GSU1293 DNA-binding response regulator, LuxR family (VIMSS) 76, 81
GSU1390 GSU1390 DNA-binding protein (NCBI) 88, 249
GSU1509 GSU1509 glycosyl transferase, group 2 family protein (VIMSS) 88, 124
GSU1564 GSU1564 Glu/Leu/Phe/Val dehydrogenase family protein (NCBI) 51, 76
GSU1638 GSU1638 conserved domain protein (NCBI) 88, 314
GSU1667 GSU1667 hypothetical protein (VIMSS) 88, 124
GSU1705 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 88, 290
GSU1761 GSU1761 cytochrome c family protein (VIMSS) 76, 214
GSU1879 GSU1879 DNA-binding response regulator (VIMSS) 7, 76
GSU1910 ilvN acetolactate synthase, small subunit (NCBI) 88, 276
GSU1962 GSU1962 glycosyl transferase, group 2 family protein (VIMSS) 88, 191
GSU2028 GSU2028 type IV pilus biogenesis protein PilQ (VIMSS) 76, 136
GSU2029 GSU2029 lipoprotein, putative (VIMSS) 76, 136
GSU2030 GSU2030 type IV pilus biogenesis protein PilO (VIMSS) 7, 76
GSU2031 GSU2031 type IV pilus biogenesis protein PilN (VIMSS) 7, 76
GSU2032 GSU2032 type IV pilus biogenesis protein PilM (VIMSS) 76, 81
GSU2045 valS valyl-tRNA synthetase (NCBI) 76, 301
GSU2060 GSU2060 pmbA protein, putative (VIMSS) 4, 88
GSU2061 argA acetyltransferase, GNAT family (NCBI) 4, 88
GSU2062 GSU2062 GGDEF domain protein (VIMSS) 4, 88
GSU2063 GSU2063 HD domain protein (NCBI) 4, 88
GSU2066 glgP glycogen phosphorylase (NCBI) 88, 201
GSU2067 GSU2067 ATPase, AAA family (VIMSS) 88, 327
GSU2068 GSU2068 6-phosphofructokinase (VIMSS) 88, 121
GSU2371 trpA tryptophan synthase, alpha subunit (NCBI) 88, 148
GSU2376 GSU2376 hypothetical protein (VIMSS) 88, 327
GSU2413 GSU2413 ABC transporter, ATP-binding protein (VIMSS) 76, 318
GSU2415 tesA lipase/acylhydrolase, putative (NCBI) 76, 176
GSU2439 relE RelE protein (NCBI) 88, 269
GSU2474 GSU2474 hypothetical protein (VIMSS) 88, 181
GSU2605 cmk cytidylate kinase (NCBI) 76, 201
GSU2608 pheA chorismate mutase/prephenate dehydratase (NCBI) 76, 81
GSU2620 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase (NCBI) 76, 158
GSU2627 bioC biotin biosynthesis protein (Dmitry Rodionov) 88, 149
GSU2628 bioH biotin biosynthesis protein (Dmitry Rodionov) 88, 149
GSU2629 bioF 8-amino-7-oxononanoate synthase (NCBI) 88, 149
GSU2631 GSU2631 conserved hypothetical protein TIGR00149 (VIMSS) 76, 88
GSU2946 tcrA DNA-binding heavy metal response regulator (NCBI) 76, 201
GSU2995 cobI precorrin-2 C20-methyltransferase (NCBI) 51, 76
GSU3208 GSU3208 conserved hypothetical protein (NCBI) 88, 121
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 GSU0280
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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