Organism : Geobacter sulfurreducens | Module List :
GSU1277 greA

transcription elongation factor GreA (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
greA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1277
(Mouseover regulator name to see its description)

GSU1277 is regulated by 17 influences and regulates 7 modules.
Regulators for GSU1277 greA (17)
Regulator Module Operator
GSU0266 19 tf
GSU1626 19 tf
GSU1687 19 tf
GSU1727 19 tf
GSU1989 19 tf
GSU2581 19 tf
GSU2831 19 tf
GSU3087 19 tf
GSU3387 19 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: GSU1277 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
2198 3.10e+03 GGGcttTT.cTtT
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2199 5.50e+03 CGGAgGgg
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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 GSU1277

GSU1277 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
greA tigr/ tigrfam
Module neighborhood information for GSU1277

GSU1277 has total of 34 gene neighbors in modules 19, 248
Gene neighbors (34)
Gene Common Name Description Module membership
GSU0117 GSU0117 aminotransferase, classes I and II (NCBI) 7, 248
GSU0161 GSU0161 hypothetical protein (VIMSS) 18, 19
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
GSU1165 ptsP phosphoenolpyruvate-protein phosphotransferase PtsP (NCBI) 19, 125
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
GSU1583 bioD dethiobiotin synthase (NCBI) 120, 248
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
GSU1591 truB tRNA pseudouridine synthase B (NCBI) 120, 248
GSU1592 rpsO ribosomal protein S15 (NCBI) 120, 248
GSU1593 pnp polyribonucleotide nucleotidyltransferase (NCBI) 120, 248
GSU1760 cyd-5 cytochrome c3 (NCBI) 30, 248
GSU1794 GSU1794 HAM1 protein (NCBI) 158, 248
GSU1808 folP dihydropteroate synthase (NCBI) 19, 144
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
GSU2072 GSU2072 1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (VIMSS) 7, 248
GSU2284 GSU2284 conserved hypothetical protein TIGR00043 (NCBI) 19, 262
GSU2625 GSU2625 transcriptional regulator, ArsR family (NCBI) 120, 248
GSU3006 cobB cobyrinic acid a,c-diamide synthase (NCBI) 30, 248
GSU3013 cgpA GTP-binding protein (NCBI) 19, 35
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
GSU3375 GSU3375 MutT/nudix family protein (VIMSS) 19, 26
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 GSU1277
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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