Organism : Geobacter sulfurreducens | Module List :
GSU0656 ilvE

branched-chain amino acid aminotransferase (NCBI)

CircVis
Functional Annotations (9)
Function System
Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase cog/ cog
branched-chain-amino-acid transaminase activity go/ molecular_function
branched chain family amino acid metabolic process go/ biological_process
Valine leucine and isoleucine degradation kegg/ kegg pathway
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Pantothenate and CoA biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
ilvE_II tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0656
(Mouseover regulator name to see its description)

GSU0656 is regulated by 21 influences and regulates 0 modules.
Regulators for GSU0656 ilvE (21)
Regulator Module Operator
GSU0013 75 tf
GSU0031 75 tf
GSU0280 75 tf
GSU0359 75 tf
GSU0366 75 tf
GSU0372 75 tf
GSU0625 75 tf
GSU1522 75 tf
GSU1727 75 tf
GSU2523 75 tf
GSU2831 75 tf
GSU3229 75 tf
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

Warning: GSU0656 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
2310 1.40e+03 CTctgcttAagTatAtCgGttaAt
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2311 8.90e+03 aTaTtAAAAaA
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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 GSU0656

GSU0656 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU0656

GSU0656 has total of 44 gene neighbors in modules 75, 183
Gene neighbors (44)
Gene Common Name Description Module membership
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
GSU0541 polA DNA polymerase I (NCBI) 164, 183
GSU0656 ilvE branched-chain amino acid aminotransferase (NCBI) 75, 183
GSU0671 rluC ribosomal large subunit pseudouridine synthase C (NCBI) 26, 183
GSU0751 GSU0751 conserved hypothetical protein (VIMSS) 147, 183
GSU0821 GSU0821 conserved hypothetical protein (VIMSS) 8, 75
GSU0825 GSU0825 pirin family protein (VIMSS) 126, 183
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
GSU1246 dgt deoxyguanosinetriphosphate triphosphohydrolase, putative (NCBI) 75, 154
GSU1262 GSU1262 membrane protein, putative (VIMSS) 75, 176
GSU1298 GSU1298 methyl-accepting chemotaxis protein (VIMSS) 126, 183
GSU1314 GSU1314 membrane protein, putative (VIMSS) 75, 136
GSU1443 GSU1443 sensor histidine kinase/response regulator (VIMSS) 183, 191
GSU1450 nth endonuclease III, putative (NCBI) 75, 227
GSU1488 GSU1488 membrane protein, putative (VIMSS) 75, 222
GSU1489 GSU1489 membrane protein, putative (VIMSS) 75, 199
GSU1491 GSU1491 type IV pilus biogenesis protein PilB (VIMSS) 51, 75
GSU1492 pilT-4 twitching motility protein PilT (NCBI) 75, 208
GSU1493 GSU1493 type IV pilus biogenesis protein PilC (VIMSS) 75, 313
GSU1517 rpmI ribosomal protein L35 (NCBI) 75, 161
GSU1527 GSU1527 conserved hypothetical protein (VIMSS) 147, 183
GSU1772 ctpA-2 carboxy-terminal processing protease (NCBI) 25, 183
GSU1809 ftsH-2 cell division protein FtsH (NCBI) 183, 207
GSU1870 GSU1870 GGDEF domain protein (VIMSS) 183, 335
GSU2102 GSU2102 pyruvate formate-lyase-activating enzyme, putative (VIMSS) 126, 183
GSU2291 GSU2291 phospho-2-dehydro-3-deoxyheptonate aldolase (VIMSS) 75, 227
GSU2414 GSU2414 membrane protein, putative (VIMSS) 164, 183
GSU2464 GSU2464 hypothetical protein (VIMSS) 156, 183
GSU2587 GSU2587 transcriptional regulator, MarR family (VIMSS) 140, 183
GSU2588 lpdA-2 alpha keto acid dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI) 75, 153
GSU2659 GSU2659 hypothetical protein (VIMSS) 183, 287
GSU2759 GSU2759 potassium efflux system protein (VIMSS) 183, 287
GSU3000 GSU3000 cbiX protein (NCBI) 183, 265
GSU3004 GSU3004 cobalt transport protein CbiM (RefSeq) 75, 89
GSU3108 rho transcription termination factor Rho (NCBI) 183, 335
GSU3128 GSU3128 hypothetical protein (VIMSS) 95, 183
GSU3160 rluC RNA pseudouridine synthase family protein (NCBI) 42, 183
GSU3203 GSU3203 outer membrane lipoprotein carrier protein LolA, putative (NCBI) 104, 183
GSU3314 GSU3314 lipoprotein, putative (VIMSS) 164, 183
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 GSU0656
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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