Organism : Geobacter sulfurreducens | Module List :
GSU3370

transcriptional regulator, GntR family (VIMSS)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3370
(Mouseover regulator name to see its description)

GSU3370 is regulated by 13 influences and regulates 23 modules.
Regulators for GSU3370 (13)
Regulator Module Operator
GSU0018 243 tf
GSU0366 243 tf
GSU1495 243 tf
GSU2524 243 tf
GSU2753 243 tf
GSU2831 243 tf
GSU3087 243 tf
GSU3370 243 tf
GSU1905 297 tf
GSU2524 297 tf
GSU2831 297 tf
GSU3087 297 tf
GSU3370 297 tf

Warning: GSU3370 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
2646 4.60e-20 GtATacTGTATACAatat
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2647 2.10e-02 ttatTT.TTaAaaca
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2752 4.10e-04 taatTgTaTacAGtAt
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2753 4.60e+01 tAaATgGCa
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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 GSU3370

GSU3370 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for GSU3370

GSU3370 has total of 35 gene neighbors in modules 243, 297
Gene neighbors (35)
Gene Common Name Description Module membership
GSU0109 atpF ATP synthase F0, B subunit (NCBI) 243, 245
GSU0110 atpH ATP synthase F1, delta subunit (NCBI) 18, 243
GSU0113 atpD ATP synthase F1, beta subunit (NCBI) 162, 243
GSU0312 GSU0312 hypothetical protein (VIMSS) 18, 243
GSU0338 nuoA-1 NADH dehydrogenase I, A subunit (NCBI) 18, 243
GSU0339 nuoB NADH dehydrogenase I, B subunit (NCBI) 297, 305
GSU0340 nuoC NADH dehydrogenase I, C subunit (NCBI) 297, 305
GSU0341 nouD NADH dehydrogenase I, D subunit (NCBI) 297, 305
GSU0342 nuoE-1 NADH dehydrogenase I, E subunit (NCBI) 230, 243
GSU0343 nouF NADH dehydrogenase I, F subunit (NCBI) 243, 305
GSU0345 nuoH-1 NADH dehydrogenase I, H subunit (NCBI) 243, 305
GSU0346 nuoI-1 NADH dehydrogenase I, I subunit (NCBI) 297, 305
GSU0347 nouJ NADH dehydrogenase I, J subunit (NCBI) 297, 305
GSU0348 nuoK NADH dehydrogenase I, K subunit (NCBI) 297, 305
GSU0349 nuoL-1 NADH dehydrogenase I, L subunit (NCBI) 297, 305
GSU0350 nuoM-1 NADH dehydrogenase I, M subunit (NCBI) 297, 305
GSU0351 nuoN-1 NADH dehydrogenase I, N subunit (NCBI) 297, 305
GSU0384 GSU0384 conserved hypothetical protein (VIMSS) 18, 243
GSU0385 GSU0385 NADH dehydrogenase subunit, putative (VIMSS) 243, 257
GSU0509 sfrA Fe(III) reductase, alpha subunit (NCBI) 101, 243
GSU0510 sfrB Fe(III) reductase, beta subunit (NCBI) 101, 243
GSU0994 fumB fumarate hydratase, class I (NCBI) 101, 243
GSU1106 GSU1106 citrate synthase (NCBI) 101, 243
GSU1451 GSU1451 3-hydroxyisobutyrate dehydrogenase family protein (VIMSS) 170, 243
GSU1465 icd isocitrate dehydrogenase, NADP-dependent (NCBI) 101, 297
GSU1466 mdh malate dehydrogenase (NCBI) 101, 297
GSU1467 GSU1467 iron-sulfur cluster-binding protein (VIMSS) 297, 305
GSU1468 GSU1468 keto/oxoacid ferredoxin oxidoreductase, alpha subunit (VIMSS) 297, 305
GSU1469 GSU1469 keto/oxoacid ferredoxin oxidoreductase, beta subunit (VIMSS) 297, 305
GSU1470 GSU1470 keto/oxoacid ferredoxin oxidoreductase, gamma subunit (VIMSS) 297, 305
GSU1647 GSU1647 hypothetical protein (VIMSS) 129, 243
GSU2206 rpsT ribosomal protein S20 (NCBI) 228, 297
GSU2602 huP-1 DNA-binding protein HU (NCBI) 5, 243
GSU2977 GSU2977 transaldolase, putative (VIMSS) 137, 243
GSU3370 GSU3370 transcriptional regulator, GntR family (VIMSS) 243, 297
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 GSU3370
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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