Organism : Geobacter sulfurreducens | Module List :
GSU2587

transcriptional regulator, MarR family (VIMSS)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA polymerase II transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription factor TFIIE complex go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription initiation from RNA polymerase II promoter go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2587
(Mouseover regulator name to see its description)

GSU2587 is regulated by 20 influences and regulates 17 modules.
Regulators for GSU2587 (20)
Regulator Module Operator
GSU0812 183 tf
GSU1268 183 tf
GSU1410 183 tf
GSU1626 183 tf
GSU1687 183 tf
GSU2523 183 tf
GSU2524 183 tf
GSU3108 183 tf
GSU3387 183 tf
GSU0205 140 tf
GSU0399 140 tf
GSU0682 140 tf
GSU0735 140 tf
GSU0951 140 tf
GSU2033 140 tf
GSU2362 140 tf
GSU2587 140 tf
GSU2915 140 tf
GSU2926 140 tf
GSU3324 140 tf

Warning: GSU2587 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
2440 1.70e+03 AtATtGaAtTaAca
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2441 2.30e+04 AAGAttAacGTgcaGGGaA
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2526 2.60e+03 TATtTtAat.gGtaa
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2527 2.50e+03 aatgataAaaCGGgTATgAgcCGg
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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 GSU2587

GSU2587 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
RNA polymerase II transcription factor activity go/ molecular_function
intracellular go/ cellular_component
transcription factor TFIIE complex go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription initiation from RNA polymerase II promoter go/ biological_process
Module neighborhood information for GSU2587

GSU2587 has total of 63 gene neighbors in modules 140, 183
Gene neighbors (63)
Gene Common Name Description Module membership
GSU0138 prfC peptide chain release factor 3 (NCBI) 140, 275
GSU0167 GSU0167 conserved hypothetical protein, truncation (NCBI) 62, 140
GSU0362 GSU0362 hypothetical protein (VIMSS) 142, 183
GSU0436 pilT-3 twitching motility protein PilT (NCBI) 78, 183
GSU0446 GSU0446 conserved hypothetical protein TIGR00046 (VIMSS) 147, 183
GSU0490 GSU0490 acetyl-CoA hydrolase/transferase family protein (VIMSS) 140, 225
GSU0541 polA DNA polymerase I (NCBI) 164, 183
GSU0602 GSU0602 conserved hypothetical protein (VIMSS) 140, 275
GSU0649 rnhB ribonuclease HII (NCBI) 42, 140
GSU0656 ilvE branched-chain amino acid aminotransferase (NCBI) 75, 183
GSU0671 rluC ribosomal large subunit pseudouridine synthase C (NCBI) 26, 183
GSU0731 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase (NCBI) 16, 140
GSU0751 GSU0751 conserved hypothetical protein (VIMSS) 147, 183
GSU0812 GSU0812 nitrogen regulation protein NtrY, putative (VIMSS) 140, 285
GSU0825 GSU0825 pirin family protein (VIMSS) 126, 183
GSU0834 GSU0834 hypothetical protein (VIMSS) 140, 190
GSU0890 ligA DNA ligase, NAD-dependent (NCBI) 183, 281
GSU0894 ppiB peptidyl-prolyl cis-trans isomerase, cyclophilin-type (NCBI) 183, 245
GSU0952 GSU0952 GGDEF domain protein (NCBI) 26, 183
GSU1067 GSU1067 conserved hypothetical protein (VIMSS) 156, 183
GSU1298 GSU1298 methyl-accepting chemotaxis protein (VIMSS) 126, 183
GSU1443 GSU1443 sensor histidine kinase/response regulator (VIMSS) 183, 191
GSU1527 GSU1527 conserved hypothetical protein (VIMSS) 147, 183
GSU1654 GSU1654 response regulator, putative (NCBI) 4, 140
GSU1772 ctpA-2 carboxy-terminal processing protease (NCBI) 25, 183
GSU1809 ftsH-2 cell division protein FtsH (NCBI) 183, 207
GSU1823 GSU1823 hypothetical protein (VIMSS) 8, 140
GSU1870 GSU1870 GGDEF domain protein (VIMSS) 183, 335
GSU2102 GSU2102 pyruvate formate-lyase-activating enzyme, putative (VIMSS) 126, 183
GSU2238 gmk guanylate kinase (NCBI) 140, 267
GSU2313 GSU2313 response regulator (VIMSS) 70, 140
GSU2316 GSU2316 mechanosensitive ion channel family protein (NCBI) 140, 257
GSU2362 GSU2362 transcriptional regulator, MarR family (VIMSS) 140, 159
GSU2414 GSU2414 membrane protein, putative (VIMSS) 164, 183
GSU2464 GSU2464 hypothetical protein (VIMSS) 156, 183
GSU2514 GSU2514 hypothetical protein (VIMSS) 128, 140
GSU2560 GSU2560 hypothetical protein (NCBI) 140, 216
GSU2562 sixA phosphohistidine phosphatase SixA (NCBI) 140, 157
GSU2587 GSU2587 transcriptional regulator, MarR family (VIMSS) 140, 183
GSU2659 GSU2659 hypothetical protein (VIMSS) 183, 287
GSU2680 GSU2680 conserved hypothetical protein (VIMSS) 140, 225
GSU2710 GSU2710 hypothetical protein (NCBI) 140, 335
GSU2749 GSU2749 NOL1/NOP2/sun family protein (VIMSS) 130, 140
GSU2759 GSU2759 potassium efflux system protein (VIMSS) 183, 287
GSU2761 GSU2761 FAD-dependent glycerol-3-phosphate dehydrogenase subunit (VIMSS) 42, 140
GSU2826 GSU2826 membrane protein, putative (VIMSS) 140, 275
GSU2893 GSU2893 hypothetical protein (VIMSS) 130, 140
GSU2978 GSU2978 hypothetical protein (VIMSS) 133, 140
GSU3000 GSU3000 cbiX protein (NCBI) 183, 265
GSU3039 GSU3039 hypothetical protein (VIMSS) 97, 140
GSU3069 murG UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI) 140, 264
GSU3072 mraY phospho-N-acetylmuramoyl-pentapeptide-transferase (NCBI) 140, 264
GSU3104 prfA peptide chain release factor 1 (NCBI) 82, 140
GSU3107 rpmE ribosomal protein L31 (NCBI) 113, 140
GSU3108 rho transcription termination factor Rho (NCBI) 183, 335
GSU3128 GSU3128 hypothetical protein (VIMSS) 95, 183
GSU3158 cysM cysteine synthase b (VIMSS) 140, 258
GSU3160 rluC RNA pseudouridine synthase family protein (NCBI) 42, 183
GSU3203 GSU3203 outer membrane lipoprotein carrier protein LolA, putative (NCBI) 104, 183
GSU3215 GSU3215 hypothetical protein (VIMSS) 113, 140
GSU3314 GSU3314 lipoprotein, putative (VIMSS) 164, 183
GSU3412 GSU3412 hypothetical protein (VIMSS) 49, 140
GSU3455 GSU3455 ABC transporter, permease protein, ABC-2 family (VIMSS) 129, 140
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 GSU2587
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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