Organism : Geobacter sulfurreducens | Module List :
GSU1992

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 GSU1992
(Mouseover regulator name to see its description)

GSU1992 is regulated by 15 influences and regulates 24 modules.
Regulators for GSU1992 (15)
Regulator Module Operator
GSU0041 264 tf
GSU1320 264 tf
GSU1569 264 tf
GSU1639 264 tf
GSU1992 264 tf
GSU2735 264 tf
GSU2809 264 tf
GSU2868 264 tf
GSU2915 264 tf
GSU0175 279 tf
GSU1218 279 tf
GSU1525 279 tf
GSU1687 279 tf
GSU1992 279 tf
GSU2964 279 tf

Warning: GSU1992 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
2688 1.80e+02 AAaAAT
Loader icon
2689 2.50e+03 tgtcatAaaAaaGattactT
Loader icon
2718 7.10e+02 AGATggcGGcGaaAATctATctAT
Loader icon
2719 3.30e+01 GcCaCAAccaTACCA
Loader icon
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 GSU1992

GSU1992 is enriched for 4 functions in 3 categories.
Module neighborhood information for GSU1992

GSU1992 has total of 46 gene neighbors in modules 264, 279
Gene neighbors (46)
Gene Common Name Description Module membership
GSU0069 GSU0069 oxidoreductase, iron-sulfur cluster-binding subunit (VIMSS) 270, 279
GSU0074 elbB enhancing lycopene biosynthesis protein 2 (NCBI) 160, 279
GSU0075 GSU0075 conserved hypothetical protein (VIMSS) 251, 279
GSU0076 GSU0076 hypothetical protein (VIMSS) 251, 279
GSU0077 GSU0077 hypothetical protein (VIMSS) 251, 279
GSU0078 GSU0078 hypothetical protein (VIMSS) 251, 279
GSU0098 GSU0098 MglB protein (VIMSS) 114, 264
GSU0104 GSU0104 response regulator, putative (VIMSS) 200, 279
GSU0388 GSU0388 conserved hypothetical protein (NCBI) 89, 264
GSU0476 GSU0476 conserved hypothetical protein (VIMSS) 77, 264
GSU0726 GSU0726 chemotaxis protein CheD, putative (VIMSS) 177, 279
GSU0780 GSU0780 formate dehydrogenase accessory protein FdhD (VIMSS) 184, 264
GSU1117 GSU1117 response regulator (VIMSS) 94, 264
GSU1118 GSU1118 universal stress protein family (VIMSS) 264, 276
GSU1119 GSU1119 sensor histidine kinase/response regulator (VIMSS) 94, 264
GSU1159 GSU1159 intracellular protease, PfpI family (NCBI) 279, 310
GSU1639 GSU1639 Rrf2 family protein (NCBI) 264, 315
GSU1640 cydA cytochrome d ubiquinol oxidase, subunit I (NCBI) 264, 315
GSU1641 cydB cytochrome d ubiquinol oxidase, subunit II (NCBI) 264, 315
GSU1817 GSU1817 outer membrane lipoprotein, Slp family, putative (VIMSS) 53, 264
GSU1867 GSU1867 hypothetical protein (VIMSS) 258, 264
GSU1949 GSU1949 hypothetical protein (VIMSS) 65, 264
GSU1992 GSU1992 transcriptional regulator, Crp/Fnr family (VIMSS) 264, 279
GSU2044 GSU2044 sensory box/GGDEF family protein (VIMSS) 100, 264
GSU2054 GSU2054 hypothetical protein (VIMSS) 151, 279
GSU2730 GSU2730 hypothetical protein (NCBI) 113, 264
GSU3063 ftsZ cell division protein FtsZ (NCBI) 230, 264
GSU3065 ftsQ cell division protein FtsQ (NCBI) 200, 264
GSU3066 ddl D-alanine--D-alanine ligase (NCBI) 35, 264
GSU3067 murB UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI) 94, 264
GSU3068 murC UDP-N-acetylmuramate--alanine ligase (NCBI) 94, 264
GSU3069 murG UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI) 140, 264
GSU3070 GSU3070 cell division protein, rodA/ftsW/spoVE family (VIMSS) 60, 264
GSU3071 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase (NCBI) 95, 264
GSU3072 mraY phospho-N-acetylmuramoyl-pentapeptide-transferase (NCBI) 140, 264
GSU3238 GSU3238 Rieske 2Fe-2S family protein (VIMSS) 95, 264
GSU3240 GSU3240 radical SAM domain protein (NCBI) 100, 264
GSU3246 GSU3246 thioredoxin peroxidase (VIMSS) 264, 315
GSU3252 GSU3252 sensor histidine kinase (VIMSS) 279, 320
GSU3253 GSU3253 response regulator (VIMSS) 100, 279
GSU3255 GSU3255 conserved hypothetical protein (NCBI) 100, 279
GSU3256 galT galactose-1-phosphate uridylyltransferase (NCBI) 188, 279
GSU3257 glgA-2 glycogen synthase (NCBI) 279, 320
GSU3258 GSU3258 hypothetical protein (VIMSS) 279, 320
GSU3342 GSU3342 conserved domain protein (NCBI) 177, 279
GSU3344 GSU3344 hypothetical protein (VIMSS) 27, 279
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 GSU1992
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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