Organism : Geobacter sulfurreducens | Module List :
GSU3421

transcriptional regulator, Crp/Fnr family (VIMSS)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3421
(Mouseover regulator name to see its description)

GSU3421 is regulated by 21 influences and regulates 25 modules.
Regulators for GSU3421 (21)
Regulator Module Operator
GSU0514 126 tf
GSU0551 126 tf
GSU0770 126 tf
GSU1687 126 tf
GSU1692 126 tf
GSU1989 126 tf
GSU1992 126 tf
GSU2262 126 tf
GSU3421 126 tf
GSU0164 164 tf
GSU0267 164 tf
GSU0470 164 tf
GSU0598 164 tf
GSU0776 164 tf
GSU1687 164 tf
GSU1989 164 tf
GSU2041 164 tf
GSU2523 164 tf
GSU2809 164 tf
GSU3060 164 tf
GSU3421 164 tf

Warning: GSU3421 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
2412 8.80e+02 CtCctGgGGggcCGg
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2413 5.60e+03 TctCcaTtTtTcCCT
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2488 8.60e-01 aTGaCTtGTatgAcAAAtTCG
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2489 9.90e-01 GCgCatCttcgCCgcCgaCgC
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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 GSU3421

GSU3421 is enriched for 4 functions in 3 categories.
Module neighborhood information for GSU3421

GSU3421 has total of 58 gene neighbors in modules 126, 164
Gene neighbors (58)
Gene Common Name Description Module membership
GSU0087 GSU0087 heterodisulfide reductase, iron-sulfur binding subunit, putative (VIMSS) 126, 214
GSU0089 GSU0089 heterodisulfide reductase subunit (VIMSS) 126, 291
GSU0090 GSU0090 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0091 GSU0091 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0213 GSU0213 radical SAM domain protein (NCBI) 126, 323
GSU0226 GSU0226 L-lactate permease, putative (VIMSS) 126, 164
GSU0227 GSU0227 type II DNA modification methyltransferase, putative (NCBI) 164, 253
GSU0457 GSU0457 lipoprotein, putative (VIMSS) 125, 164
GSU0458 GSU0458 (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase, putative (VIMSS) 125, 164
GSU0524 GSU0524 conserved hypothetical protein (VIMSS) 47, 164
GSU0526 GSU0526 conserved hypothetical protein (VIMSS) 126, 281
GSU0541 polA DNA polymerase I (NCBI) 164, 183
GSU0825 GSU0825 pirin family protein (VIMSS) 126, 183
GSU0841 GSU0841 sigma-54 dependent DNA-binding response regulator (VIMSS) 164, 281
GSU0854 GSU0854 membrane protein (NCBI) 65, 164
GSU0858 GSU0858 TonB-dependent receptor, putative (VIMSS) 9, 164
GSU0860 GSU0860 methylenetetrahydrofolate reductase family protein (VIMSS) 126, 144
GSU0862 folD-2 folD bifunctional protein (NCBI) 46, 126
GSU0903 GSU0903 None 126, 317
GSU0932 uraA uracil permease (NCBI) 147, 164
GSU0934 GSU0934 hypothetical protein (VIMSS) 8, 164
GSU0997 mutM formamidopyrimidine-DNA glycosylase (NCBI) 40, 164
GSU1009 hflX GTP-binding protein (NCBI) 164, 253
GSU1053 GSU1053 sensory box protein (VIMSS) 122, 126
GSU1124 coaBC phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI) 126, 295
GSU1180 ftsH-1 cell division protein FtsH (NCBI) 112, 126
GSU1274 GSU1274 radical SAM domain protein (NCBI) 126, 208
GSU1297 GSU1297 ISGsu2, transposase (VIMSS) 72, 164
GSU1298 GSU1298 methyl-accepting chemotaxis protein (VIMSS) 126, 183
GSU1377 GSU1377 3-hydroxybutyryl-CoA dehydratase (VIMSS) 11, 126
GSU1461 pyrF orotidine 5`-phosphate decarboxylase (NCBI) 126, 233
GSU1535 recD exodeoxyribonuclease V, alpha subunit (NCBI) 126, 336
GSU1562 GSU1562 conserved hypothetical protein TIGR00106 (VIMSS) 164, 253
GSU1563 GSU1563 hypothetical protein (VIMSS) 97, 164
GSU1710 GSU1710 None 126, 249
GSU2047 GSU2047 conserved hypothetical protein (VIMSS) 26, 126
GSU2050 secA preprotein translocase, SecA subunit (NCBI) 91, 126
GSU2102 GSU2102 pyruvate formate-lyase-activating enzyme, putative (VIMSS) 126, 183
GSU2214 cheB-3 protein-glutamate methylesterase (NCBI) 126, 295
GSU2222 cheA-2 chemotaxis protein CheA (NCBI) 126, 222
GSU2239 GSU2239 conserved hypothetical protein TIGR00255 (VIMSS) 47, 164
GSU2272 GSU2272 lipoprotein, putative (VIMSS) 80, 126
GSU2337 GSU2337 glycosyl transferase, group 20 family protein (NCBI) 47, 164
GSU2375 GSU2375 None 126, 322
GSU2414 GSU2414 membrane protein, putative (VIMSS) 164, 183
GSU2674 GSU2674 hypothetical protein (VIMSS) 164, 323
GSU2683 panE 2-dehydropantoate 2-reductase (VIMSS) 47, 164
GSU2736 GSU2736 hypothetical protein (VIMSS) 164, 327
GSU2879 leuB 3-isopropylmalate dehydrogenase (NCBI) 126, 233
GSU3049 GSU3049 hypothetical protein (VIMSS) 160, 164
GSU3062 GSU3062 radical SAM domain protein (NCBI) 42, 126
GSU3133 GSU3133 penicillin-binding protein, 1A family (VIMSS) 47, 164
GSU3147 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB (NCBI) 164, 201
GSU3260 GSU3260 phosphoserine aminotransferase, putative (VIMSS) 35, 126
GSU3314 GSU3314 lipoprotein, putative (VIMSS) 164, 183
GSU3371 GSU3371 AP endonuclease, family 2 (NCBI) 47, 164
GSU3411 pcrA ATP-dependent DNA helicase PcrA, putative (NCBI) 164, 281
GSU3421 GSU3421 transcriptional regulator, Crp/Fnr family (VIMSS) 126, 164
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 GSU3421
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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