Organism : Geobacter sulfurreducens | Module List :
GSU1201 greB

transcription elongation factor GreB (NCBI)

CircVis
Functional Annotations (5)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
greB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1201
(Mouseover regulator name to see its description)

GSU1201 is regulated by 18 influences and regulates 22 modules.
Regulators for GSU1201 greB (18)
Regulator Module Operator
GSU0031 106 tf
GSU0187 106 tf
GSU0581 106 tf
GSU0732 106 tf
GSU1201 106 tf
GSU1525 106 tf
GSU1692 106 tf
GSU2753 106 tf
GSU2964 106 tf
GSU0581 192 tf
GSU1201 192 tf
GSU1525 192 tf
GSU1626 192 tf
GSU1727 192 tf
GSU1934 192 tf
GSU2520 192 tf
GSU2523 192 tf
GSU2524 192 tf

Warning: GSU1201 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
2372 2.60e+01 aAAg.GtTtG.CaTT
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2373 1.30e+02 TgGTgAtAAaA
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2544 7.70e+01 TgaaActaAtGttc.AAtTgAC
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2545 9.20e+01 AatCTTCttacATacA
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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 GSU1201

GSU1201 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
greB tigr/ tigrfam
Module neighborhood information for GSU1201

GSU1201 has total of 36 gene neighbors in modules 106, 192
Gene neighbors (36)
Gene Common Name Description Module membership
GSU0004 gyrA DNA gyrase, A subunit (NCBI) 74, 192
GSU0215 folD-1 folD bifunctional protein (NCBI) 39, 106
GSU0870 mutT mutator mutT protein (NCBI) 106, 306
GSU0882 GSU0882 conserved hypothetical protein (VIMSS) 31, 106
GSU0883 GSU0883 ferric enterobactin receptor, putative (VIMSS) 139, 192
GSU1103 GSU1103 long-chain-fatty-acid--CoA ligase, putative (NCBI) 168, 192
GSU1200 rpsA ribosomal protein S1 (NCBI) 74, 192
GSU1201 greB transcription elongation factor GreB (NCBI) 106, 192
GSU1222 GSU1222 histone deacetylase/AcuC/AphA family protein (VIMSS) 106, 181
GSU1223 GSU1223 hypothetical protein (VIMSS) 106, 319
GSU1319 GSU1319 sensor histidine kinase (VIMSS) 106, 181
GSU1365 GSU1365 Mrr restriction system protein, putative (NCBI) 83, 106
GSU1524 pcm protein-L-isoaspartate O-methyltransferase (NCBI) 102, 192
GSU1525 rpoD RNA polymerase sigma-70 factor family (NCBI) 74, 192
GSU1526 apt adenine phosphoribosyltransferase (NCBI) 31, 192
GSU1652 GSU1652 hypothetical protein (VIMSS) 106, 276
GSU1797 GSU1797 ComEA-related protein (VIMSS) 106, 306
GSU1806 GSU1806 hypothetical protein (VIMSS) 83, 106
GSU1908 GSU1908 phosphatidylserine decarboxylase, putative (NCBI) 39, 106
GSU1927 GSU1927 sensory box/response regulator (VIMSS) 30, 106
GSU1934 GSU1934 transcriptional activator, putative, Baf family (VIMSS) 31, 192
GSU2055 GSU2055 extracellular solute-binding protein, family 7 (VIMSS) 192, 227
GSU2104 GSU2104 lipoprotein, putative (VIMSS) 106, 276
GSU2428 pyc pyruvate carboxylase (NCBI) 168, 192
GSU2516 GSU2516 Rhodanese-like domain protein (VIMSS) 168, 192
GSU2518 GSU2518 conserved hypothetical protein (VIMSS) 168, 192
GSU2522 GSU2522 hypothetical protein (VIMSS) 168, 192
GSU2601 GSU2601 TPR domain/SEC-C motif domain protein (NCBI) 39, 106
GSU3275 GSU3275 hypothetical protein (NCBI) 98, 192
GSU3299 mmdA carboxyl transferase domain protein (NCBI) 30, 106
GSU3301 GSU3301 conserved hypothetical protein (NCBI) 106, 248
GSU3303 GSU3303 methylmalonyl-CoA epimerase (VIMSS) 106, 230
GSU3305 GSU3305 hypothetical protein (VIMSS) 106, 162
GSU3306 GSU3306 hypothetical protein (VIMSS) 30, 106
GSU3393 GSU3393 branched-chain amino acid ABC transporter, permease protein (NCBI) 74, 192
GSU3464 gidA glucose inhibited division protein A (NCBI) 106, 209
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 GSU1201
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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