Organism : Geobacter sulfurreducens | Module List :
GSU1934

transcriptional activator, putative, Baf family (VIMSS)

CircVis
Functional Annotations (7)
Function System
Putative transcriptional regulator, homolog of Bvg accessory factor cog/ cog
pantothenate kinase activity go/ molecular_function
transcription activator activity go/ molecular_function
positive regulation of transcription, DNA-dependent go/ biological_process
Pantothenate and CoA biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
baf tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1934
(Mouseover regulator name to see its description)

GSU1934 is regulated by 18 influences and regulates 39 modules.
Regulators for GSU1934 (18)
Regulator Module Operator
GSU0031 31 tf
GSU0187 31 tf
GSU0581 31 tf
GSU1201 31 tf
GSU1525 31 tf
GSU1831 31 tf
GSU1934 31 tf
GSU2753 31 tf
GSU3045 31 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: GSU1934 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
2222 1.80e+03 aaAtTtCAaccagTTgaaccTTT
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2223 1.80e+04 CCATGacagtaTCAcc
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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 GSU1934

GSU1934 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Putative transcriptional regulator, homolog of Bvg accessory factor cog/ cog
pantothenate kinase activity go/ molecular_function
transcription activator activity go/ molecular_function
positive regulation of transcription, DNA-dependent go/ biological_process
Pantothenate and CoA biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
baf tigr/ tigrfam
Module neighborhood information for GSU1934

GSU1934 has total of 32 gene neighbors in modules 31, 192
Gene neighbors (32)
Gene Common Name Description Module membership
GSU0003 gyrB DNA gyrase, B subunit (NCBI) 31, 39
GSU0004 gyrA DNA gyrase, A subunit (NCBI) 74, 192
GSU0633 GSU0633 glycosyl transferase, group 2 family protein (VIMSS) 31, 306
GSU0882 GSU0882 conserved hypothetical protein (VIMSS) 31, 106
GSU0883 GSU0883 ferric enterobactin receptor, putative (VIMSS) 139, 192
GSU1023 glgA-1 glycogen synthase (NCBI) 31, 93
GSU1074 GSU1074 conserved hypothetical protein TIGR01033 (VIMSS) 31, 260
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
GSU1284 GSU1284 cytochrome c, putative (VIMSS) 31, 162
GSU1424 GSU1424 hypothetical protein (VIMSS) 31, 102
GSU1425 lgt prolipoprotein diacylglyceryl transferase (NCBI) 31, 83
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
GSU1811 GSU1811 conserved hypothetical protein (VIMSS) 31, 316
GSU1813 GSU1813 hypothetical protein (VIMSS) 31, 306
GSU1814 GSU1814 septum formation initiator family protein (NCBI) 31, 102
GSU1815 GSU1815 NAD-dependent epimerase/dehydratase family protein (VIMSS) 31, 306
GSU1896 kdsB 3-deoxy-D-manno-octulosonate cytidylyltransferase (NCBI) 31, 306
GSU1900 GSU1900 transporter, putative (VIMSS) 31, 162
GSU1934 GSU1934 transcriptional activator, putative, Baf family (VIMSS) 31, 192
GSU2055 GSU2055 extracellular solute-binding protein, family 7 (VIMSS) 192, 227
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
GSU2604 lytB penicillin tolerance protein LytB (NCBI) 31, 74
GSU3275 GSU3275 hypothetical protein (NCBI) 98, 192
GSU3391 GSU3391 branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 31, 74
GSU3393 GSU3393 branched-chain amino acid ABC transporter, permease protein (NCBI) 74, 192
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 GSU1934
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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