Organism : Geobacter sulfurreducens | Module List :
GSU0147 recX

regulatory protein RecX (NCBI)

CircVis
Functional Annotations (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
regulation of DNA repair go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0147
(Mouseover regulator name to see its description)

GSU0147 is regulated by 17 influences and regulates 14 modules.
Regulators for GSU0147 recX (17)
Regulator Module Operator
GSU0178 198 tf
GSU0736 198 tf
GSU1320 198 tf
GSU1495 198 tf
GSU1569 198 tf
GSU2041 198 tf
GSU3370 198 tf
GSU3387 198 tf
GSU0063 338 tf
GSU0147 338 tf
GSU0372 338 tf
GSU1495 338 tf
GSU2041 338 tf
GSU2113 338 tf
GSU2177 338 tf
GSU2670 338 tf
GSU3363 338 tf

Warning: GSU0147 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
2556 2.90e+03 catCCgG...gaaaggtcTct
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2557 5.00e+03 atacaTGGAcAAaGA
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2832 4.50e+03 tTgcAtTtTTcTga
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2833 1.90e+01 aacAAtatAActA.ttaca.cttc
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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 GSU0147

GSU0147 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
regulation of DNA repair go/ biological_process
Module neighborhood information for GSU0147

GSU0147 has total of 45 gene neighbors in modules 198, 338
Gene neighbors (45)
Gene Common Name Description Module membership
GSU0102 selB selenocysteine-specific translation elongation factor (NCBI) 335, 338
GSU0127 GSU0127 conserved hypothetical protein (VIMSS) 198, 201
GSU0137 GSU0137 hypothetical protein (NCBI) 198, 226
GSU0147 recX regulatory protein RecX (NCBI) 198, 338
GSU0257 GSU0257 conserved hypothetical protein (VIMSS) 198, 222
GSU0295 cheR-1 chemotaxis protein methyltransferase CheR (NCBI) 278, 338
GSU0465 efp-1 translation elongation factor P (NCBI) 198, 338
GSU0808 pleD GGDEF domain protein (NCBI) 47, 338
GSU0953 GSU0953 hypothetical protein (VIMSS) 87, 198
GSU0954 GSU0954 conserved hypothetical protein (VIMSS) 260, 338
GSU1033 GSU1033 methyl-accepting chemotaxis protein (VIMSS) 36, 198
GSU1112 mtaP methylthioadenosine phosphorylase (NCBI) 68, 338
GSU1191 GSU1191 hypothetical protein (VIMSS) 335, 338
GSU1286 cheY-2 chemotaxis protein CheY (NCBI) 198, 221
GSU1364 GSU1364 HNH endonuclease family protein (NCBI) 199, 338
GSU1366 GSU1366 hypothetical protein (VIMSS) 143, 338
GSU1367 GSU1367 hypothetical protein (VIMSS) 301, 338
GSU1368 GSU1368 hypothetical protein (VIMSS) 301, 338
GSU1369 GSU1369 conserved hypothetical protein (VIMSS) 68, 338
GSU1435 GSU1435 peptide ABC transporter, permease protein (VIMSS) 104, 338
GSU1486 GSU1486 MttB family protein (VIMSS) 319, 338
GSU1487 ribF riboflavin biosynthesis protein RibF (NCBI) 301, 338
GSU1494 GSU1494 sensory box histidine kinase (VIMSS) 198, 338
GSU1495 GSU1495 sigma-54 dependent DNA-binding response regulator (VIMSS) 87, 198
GSU1545 GSU1545 transporter, LysE family (VIMSS) 181, 338
GSU1568 GSU1568 conserved hypothetical protein (VIMSS) 71, 198
GSU1611 GSU1611 AcrB/AcrD/AcrF family protein (VIMSS) 278, 338
GSU1612 gpm phosphoglycerate mutase (NCBI) 47, 338
GSU1674 GSU1674 hypothetical protein (VIMSS) 260, 338
GSU1686 GSU1686 cytidine/deoxycytidylate deaminase family protein (VIMSS) 198, 221
GSU1810 GSU1810 cell cycle protein MesJ, putative (VIMSS) 15, 198
GSU1838 hrpB ATP-dependent helicase HrpB (NCBI) 147, 338
GSU1923 GSU1923 membrane protein, putative (VIMSS) 47, 338
GSU2088 GSU2088 glycosyl transferase, group 2 family protein (VIMSS) 47, 338
GSU2114 GSU2114 hypothetical protein (VIMSS) 278, 338
GSU2212 cheY-5 chemotaxis protein CheY (NCBI) 198, 218
GSU2225 b2511 GTP-binding protein Era, putative (NCBI) 198, 260
GSU2278 prfB peptide chain release factor 2 (NCBI) 198, 213
GSU2293 GSU2293 hypothetical protein (VIMSS) 181, 338
GSU2465 lipB metallo-beta-lactamase family protein (NCBI) 15, 198
GSU2477 GSU2477 TPR domain/radical SAM/B12 binding domain protein (NCBI) 59, 198
GSU2632 GSU2632 GGDEF domain protein (NCBI) 84, 338
GSU2677 GSU2677 membrane protein, putative (VIMSS) 47, 338
GSU2693 GSU2693 response regulator (VIMSS) 71, 338
GSU3465 trmE tRNA modification GTPase TrmE (NCBI) 43, 338
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 GSU0147
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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