Organism : Geobacter sulfurreducens | Module List :
GSU2262 degT

pleiotropic regulatory protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis cog/ cog
catalytic activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2262
(Mouseover regulator name to see its description)

GSU2262 is regulated by 19 influences and regulates 19 modules.
Regulators for GSU2262 degT (19)
Regulator Module Operator
GSU0013 28 tf
GSU0366 28 tf
GSU1218 28 tf
GSU1687 28 tf
GSU1727 28 tf
GSU2149 28 tf
GSU2581 28 tf
GSU2666 28 tf
GSU0013 214 tf
GSU0514 214 tf
GSU0551 214 tf
GSU0770 214 tf
GSU1270 214 tf
GSU1382 214 tf
GSU1692 214 tf
GSU2202 214 tf
GSU2262 214 tf
GSU2571 214 tf
GSU2980 214 tf

Warning: GSU2262 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
2216 5.90e+00 aGtcAAgaaaAAa
Loader icon
2217 5.90e+02 attTtcaAgca.TTt
Loader icon
2588 7.60e+00 tGCAag.acAAa.aggagAagA
Loader icon
2589 9.30e+01 CcctttC.ca.CcgtTgAaCAca
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 GSU2262

GSU2262 is enriched for 3 functions in 3 categories.
Module neighborhood information for GSU2262

GSU2262 has total of 45 gene neighbors in modules 28, 214
Gene neighbors (45)
Gene Common Name Description Module membership
GSU0023 GSU0023 TPR domain protein (NCBI) 111, 214
GSU0087 GSU0087 heterodisulfide reductase, iron-sulfur binding subunit, putative (VIMSS) 126, 214
GSU0088 GSU0088 heterodisulfide reductase subunit (VIMSS) 169, 214
GSU0090 GSU0090 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0091 GSU0091 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0092 GSU0092 heterodisulfide reductase subunit (NCBI) 127, 214
GSU0159 dapA dihydrodipicolinate synthase (NCBI) 101, 214
GSU0320 GSU0320 hypothetical protein (VIMSS) 28, 332
GSU0325 GSU0325 general secretion pathway protein H, putative (NCBI) 28, 328
GSU0327 hofF general secretion pathway protein F (NCBI) 28, 263
GSU0329 GSU0329 general secretion pathway protein D, putative (VIMSS) 28, 245
GSU0674 hcP-1 hydroxylamine reductase (RefSeq) 16, 214
GSU0792 GSU0792 conserved hypothetical protein (VIMSS) 22, 214
GSU0864 GSU0864 conserved hypothetical protein TIGR00251 (VIMSS) 101, 214
GSU0865 GSU0865 cell division protein DivIVA, putative (VIMSS) 111, 214
GSU1177 frdA fumarate reductase, flavoprotein subunit (NCBI) 101, 214
GSU1245 GSU1245 fructose-bisphosphate aldolase, class-II, putative (VIMSS) 28, 328
GSU1322 ccdA cytochrome c biogenesis protein CcdA (NCBI) 153, 214
GSU1334 GSU1334 cytochrome c family protein (NCBI) 137, 214
GSU1555 GSU1555 sensory box histidine kinase/response regulator (VIMSS) 153, 214
GSU1607 glyA Serine hydroxymethyltransferase (VIMSS) 28, 227
GSU1628 GSU1628 phosphoglycerate kinase/triosephosphate isomerase (VIMSS) 214, 238
GSU1761 GSU1761 cytochrome c family protein (VIMSS) 76, 214
GSU2049 argJ glutamate N-acetyltransferase/amino-acid acetyltransferase (NCBI) 91, 214
GSU2255 GSU2255 conserved hypothetical protein (VIMSS) 28, 214
GSU2257 GSU2257 conserved hypothetical protein (VIMSS) 28, 277
GSU2258 lpxK tetraacyldisaccharide 4'-kinase (NCBI) 28, 277
GSU2259 GSU2259 3-deoxy-D-manno-octulosonic-acid transferase, putative (VIMSS) 28, 277
GSU2260 GSU2260 ABC transporter, ATP-binding protein, MsbA family (VIMSS) 28, 214
GSU2261 lpxB lipid A disaccharide synthase (lpxB) (NCBI) 214, 262
GSU2262 degT pleiotropic regulatory protein (NCBI) 28, 214
GSU2263 GSU2263 oxidoreductase, Gfo/Idh/MocA family (VIMSS) 3, 28
GSU2265 fabZ (3R)-hydroxymyristoyl-(acyl-carrier-protein) dehydratase (VIMSS) 28, 277
GSU2267 GSU2267 outer membrane protein, putative (VIMSS) 28, 277
GSU2268 GSU2268 outer membrane protein, putative (VIMSS) 207, 214
GSU2269 GSU2269 ABC transporter, ATP-binding protein (VIMSS) 12, 214
GSU2271 lysS lysyl-tRNA synthetase (NCBI) 28, 263
GSU2556 GSU2556 peptidase, U32 family (VIMSS) 28, 328
GSU2731 ferA polyheme membrane-associated cytochrome c (NCBI) 195, 214
GSU2732 GSU2732 cytochrome c family protein (NCBI) 195, 214
GSU2733 GSU2733 hypothetical protein (VIMSS) 195, 214
GSU2737 GSU2737 polyheme membrane-associated cytochrome c (VIMSS) 195, 214
GSU2739 GSU2739 hypothetical protein (VIMSS) 195, 214
GSU3210 nadD nicotinate (nicotinamide) nucleotide adenylyltransferase (NCBI) 160, 214
GSU3408 GSU3408 L-threonine aldolase, low-specificity (VIMSS) 3, 28
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 GSU2262
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