Organism : Geobacter sulfurreducens | Module List :
GSU3206 dksA

dnaK suppressor protein, putative (NCBI)

CircVis
Functional Annotations (2)
Function System
DnaK suppressor protein cog/ cog
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3206
(Mouseover regulator name to see its description)

GSU3206 is regulated by 17 influences and regulates 7 modules.
Regulators for GSU3206 dksA (17)
Regulator Module Operator
GSU0164 35 tf
GSU0300 35 tf
GSU1003 35 tf
GSU1250 35 tf
GSU1863 35 tf
GSU2571 35 tf
GSU2625 35 tf
GSU3206 35 tf
GSU3217 35 tf
GSU0079 18 tf
GSU0207 18 tf
GSU1250 18 tf
GSU1626 18 tf
GSU1727 18 tf
GSU1905 18 tf
GSU2524 18 tf
GSU2831 18 tf

Warning: GSU3206 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
2196 3.70e-02 tacTtTtttcAttttT
Loader icon
2197 9.70e-04 AtGtcAatgcCtTTttGccg
Loader icon
2230 1.50e+01 Aat.c.tTgaAAAA.
Loader icon
2231 3.10e+03 CTGATTTT
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 GSU3206

GSU3206 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
DnaK suppressor protein cog/ cog
zinc ion binding go/ molecular_function
Module neighborhood information for GSU3206

GSU3206 has total of 49 gene neighbors in modules 18, 35
Gene neighbors (49)
Gene Common Name Description Module membership
GSU0006 gpsA glycerol-3-phosphate dehydrogenase (NAD(P)+) (NCBI) 35, 254
GSU0079 GSU0079 transcriptional regulator, Cro/CI family (VIMSS) 3, 18
GSU0110 atpH ATP synthase F1, delta subunit (NCBI) 18, 243
GSU0145 recA recA protein (NCBI) 35, 233
GSU0161 GSU0161 hypothetical protein (VIMSS) 18, 19
GSU0180 GSU0180 conserved hypothetical protein (VIMSS) 35, 202
GSU0207 GSU0207 cold-shock domain family protein (VIMSS) 18, 116
GSU0303 GSU0303 sensory box protein (VIMSS) 22, 35
GSU0312 GSU0312 hypothetical protein (VIMSS) 18, 243
GSU0335 GSU0335 hypothetical protein (VIMSS) 35, 170
GSU0338 nuoA-1 NADH dehydrogenase I, A subunit (NCBI) 18, 243
GSU0384 GSU0384 conserved hypothetical protein (VIMSS) 18, 243
GSU0390 GSU0390 conserved hypothetical protein (VIMSS) 11, 18
GSU0507 GSU0507 membrane protein, putative (NCBI) 18, 238
GSU0511 GSU0511 conserved domain protein (NCBI) 35, 231
GSU0592 GSU0592 cytochrome c family protein (NCBI) 18, 116
GSU0660 ispE 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI) 18, 228
GSU0661 prsA ribose-phosphate pyrophosphokinase (NCBI) 35, 81
GSU0664 ychF GTP binding protein YchF (NCBI) 35, 161
GSU0888 GSU0888 hypothetical protein (NCBI) 35, 202
GSU0962 GSU0962 sensor histidine kinase (VIMSS) 18, 42
GSU1073 GSU1073 conserved hypothetical protein (VIMSS) 35, 260
GSU1230 GSU1230 conserved hypothetical protein (VIMSS) 35, 205
GSU1234 sppA-2 signal peptide peptidase SppA, 36K type (NCBI) 35, 88
GSU1292 GSU1292 sensory box histidine kinase (VIMSS) 35, 295
GSU1336 GSU1336 membrane protein, TerC family (NCBI) 18, 207
GSU1386 GSU1386 conserved hypothetical protein (VIMSS) 18, 315
GSU1459 ispG 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate (NCBI) 35, 245
GSU1598 GSU1598 conserved hypothetical protein (NCBI) 35, 267
GSU1672 hprA glycerate dehydrogenase (NCBI) 35, 314
GSU1712 GSU1712 hypothetical protein (VIMSS) 18, 42
GSU1781 GSU1781 hypothetical protein (VIMSS) 17, 18
GSU1784 GSU1784 type IV pilus biogenesis protein PilC, putative (VIMSS) 17, 18
GSU1795 rph ribonuclease PH (NCBI) 35, 158
GSU1825 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (VIMSS) 35, 267
GSU1996 GSU1996 cytochrome c family protein (NCBI) 35, 154
GSU2234 rpmB ribosomal protein L28 (NCBI) 35, 340
GSU2643 GSU2643 cytochrome c family protein (NCBI) 18, 136
GSU2807 GSU2807 conserved hypothetical protein (VIMSS) 35, 202
GSU3013 cgpA GTP-binding protein (NCBI) 19, 35
GSU3066 ddl D-alanine--D-alanine ligase (NCBI) 35, 264
GSU3117 ssb-2 single-strand binding protein (NCBI) 35, 228
GSU3132 huP-2 DNA-binding protein HU (NCBI) 35, 116
GSU3206 dksA dnaK suppressor protein, putative (NCBI) 18, 35
GSU3260 GSU3260 phosphoserine aminotransferase, putative (VIMSS) 35, 126
GSU3292 GSU3292 transcriptional regulator, Fur family (VIMSS) 35, 202
GSU3293 GSU3293 conserved hypothetical protein (VIMSS) 35, 315
GSU3405 GSU3405 amino acid ABC transporter, permease protein (VIMSS) 11, 18
GSU3407 GSU3407 membrane protein, putative (VIMSS) 18, 103
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 GSU3206
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