Organism : Geobacter sulfurreducens | Module List :
GSU2625

transcriptional regulator, ArsR family (NCBI)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulators 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 GSU2625
(Mouseover regulator name to see its description)

GSU2625 is regulated by 20 influences and regulates 15 modules.
Regulators for GSU2625 (20)
Regulator Module Operator
GSU0207 120 tf
GSU0366 120 tf
GSU0598 120 tf
GSU1586 120 tf
GSU1863 120 tf
GSU1887 120 tf
GSU2625 120 tf
GSU2787 120 tf
GSU2831 120 tf
GSU2868 120 tf
GSU3127 120 tf
GSU3229 120 tf
GSU0581 248 tf
GSU1277 248 tf
GSU1483 248 tf
GSU1586 248 tf
GSU2625 248 tf
GSU2753 248 tf
GSU2831 248 tf
GSU3298 248 tf

Warning: GSU2625 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
2400 1.50e-09 CAAGtAaTTATTTTGATaaACaAa
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2401 2.10e-02 actaatcCtatCa.gAgaaA.tgG
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2656 1.40e+00 AAaAaagC
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2657 3.00e+04 ATTTGcTaCaTCaAAATAAT
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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 GSU2625

GSU2625 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU2625

GSU2625 has total of 35 gene neighbors in modules 120, 248
Gene neighbors (35)
Gene Common Name Description Module membership
GSU0117 GSU0117 aminotransferase, classes I and II (NCBI) 7, 248
GSU0191 GSU0191 cold-shock domain family protein (VIMSS) 16, 248
GSU0581 GSU0581 cold-shock domain family protein (VIMSS) 102, 248
GSU0906 rpsU-1 ribosomal protein S21 (NCBI) 11, 248
GSU1277 greA transcription elongation factor GreA (NCBI) 19, 248
GSU1278 GSU1278 conserved hypothetical protein (VIMSS) 170, 248
GSU1317 ispB octaprenyl-diphosphate synthase (NCBI) 233, 248
GSU1318 GSU1318 hypothetical protein (VIMSS) 83, 248
GSU1582 bioA adenosylmethionine--8-amino-7-oxononanoate aminotransferase (VIMSS) 120, 280
GSU1583 bioD dethiobiotin synthase (NCBI) 120, 248
GSU1584 bioB biotin synthetase (Dmitry Rodionov) 120, 315
GSU1585 GSU1585 conserved hypothetical protein (VIMSS) 120, 248
GSU1586 nusA N utilization substance protein A (NCBI) 120, 248
GSU1587 GSU1587 ribosomal protein L7Ae family protein (NCBI) 120, 248
GSU1588 infB translation initiation factor IF-2 (NCBI) 120, 248
GSU1589 rbfA ribosome-binding factor A (NCBI) 120, 248
GSU1590 GSU1590 DHH family/DHHA1 domain protein (NCBI) 17, 120
GSU1591 truB tRNA pseudouridine synthase B (NCBI) 120, 248
GSU1592 rpsO ribosomal protein S15 (NCBI) 120, 248
GSU1593 pnp polyribonucleotide nucleotidyltransferase (NCBI) 120, 248
GSU1594 GSU1594 peptidase, M16 family (VIMSS) 17, 120
GSU1596 GSU1596 Sua5/YciO/YrdC/YwlC family protein (VIMSS) 17, 120
GSU1597 GSU1597 hypothetical protein (VIMSS) 17, 120
GSU1760 cyd-5 cytochrome c3 (NCBI) 30, 248
GSU1794 GSU1794 HAM1 protein (NCBI) 158, 248
GSU1907 pssA CDP-diacylglycerol--serineO-phosphatidyltransferase (NCBI) 102, 248
GSU1918 frr ribosome recycling factor (NCBI) 230, 248
GSU1925 GSU1925 transport-associated domain protein (NCBI) 120, 248
GSU1926 GSU1926 conserved hypothetical protein (VIMSS) 60, 120
GSU2072 GSU2072 1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (VIMSS) 7, 248
GSU2625 GSU2625 transcriptional regulator, ArsR family (NCBI) 120, 248
GSU3006 cobB cobyrinic acid a,c-diamide synthase (NCBI) 30, 248
GSU3298 GSU3298 transcriptional regulator, Cro/CI family (VIMSS) 7, 248
GSU3301 GSU3301 conserved hypothetical protein (NCBI) 106, 248
GSU3365 cysS cysteinyl-tRNA synthetase (NCBI) 83, 248
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 GSU2625
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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