Organism : Geobacter sulfurreducens | Module List :
GSU2306 purE-2

phosphoribosylaminoimidazole carboxylase, catalytic subunit (NCBI)

CircVis
Functional Annotations (5)
Function System
Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase cog/ cog
phosphoribosylaminoimidazole carboxylase activity go/ molecular_function
'de novo' IMP biosynthetic process go/ biological_process
phosphoribosylaminoimidazole carboxylase complex go/ cellular_component
purE tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2306
(Mouseover regulator name to see its description)

GSU2306 is regulated by 26 influences and regulates 0 modules.
Regulators for GSU2306 purE-2 (26)
Regulator Module Operator
GSU0178 91 tf
GSU0207 91 tf
GSU0284 91 tf
GSU0581 91 tf
GSU0598 91 tf
GSU1268 91 tf
GSU1992 91 tf
GSU2041 91 tf
GSU2735 91 tf
GSU2741 91 tf
GSU2779 91 tf
GSU2980 91 tf
GSU3421 91 tf
GSU0178 111 tf
GSU0187 111 tf
GSU0682 111 tf
GSU1129 111 tf
GSU1268 111 tf
GSU1342 111 tf
GSU1687 111 tf
GSU1692 111 tf
GSU1992 111 tf
GSU2980 111 tf
GSU3041 111 tf
GSU3060 111 tf
GSU3421 111 tf

Warning: GSU2306 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
2342 4.20e+03 cAaGgaGA
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2343 2.20e+02 ATttaA.tGAGca.TTCCG
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2382 3.30e+03 TaTT.CatGcAGTTa
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2383 9.40e+03 ctaTtTg.AAtaattCgcgTT
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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 GSU2306

GSU2306 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase cog/ cog
phosphoribosylaminoimidazole carboxylase activity go/ molecular_function
'de novo' IMP biosynthetic process go/ biological_process
phosphoribosylaminoimidazole carboxylase complex go/ cellular_component
purE tigr/ tigrfam
Module neighborhood information for GSU2306

GSU2306 has total of 32 gene neighbors in modules 91, 111
Gene neighbors (32)
Gene Common Name Description Module membership
GSU0023 GSU0023 TPR domain protein (NCBI) 111, 214
GSU0119 GSU0119 glyoxalase family protein (NCBI) 74, 111
GSU0135 hemB delta-aminolevulinic acid dehydratase (NCBI) 91, 160
GSU0210 GSU0210 conserved hypothetical protein (VIMSS) 46, 91
GSU0331 htrA trypsin domain/PDZ domain protein (NCBI) 91, 292
GSU0332 pepA aminopeptidase A/I (NCBI) 91, 111
GSU0798 GSU0798 amino acid ABC transporter, ATP-binding protein (VIMSS) 111, 196
GSU0800 GSU0800 amino acid ABC transporter, periplasmic amino acid-binding protein (VIMSS) 91, 111
GSU0865 GSU0865 cell division protein DivIVA, putative (VIMSS) 111, 214
GSU1091 GSU1091 lipoprotein, putative (NCBI) 91, 111
GSU1166 GSU1166 TPR domain protein (NCBI) 80, 111
GSU1283 GSU1283 hypothetical protein (VIMSS) 91, 111
GSU1694 GSU1694 hydrolase, haloacid dehalogenase-like family (VIMSS) 111, 239
GSU2020 accB acetyl-CoA carboxylase, biotin carboxyl carrier protein (NCBI) 91, 309
GSU2049 argJ glutamate N-acetyltransferase/amino-acid acetyltransferase (NCBI) 91, 214
GSU2050 secA preprotein translocase, SecA subunit (NCBI) 91, 126
GSU2090 GSU2090 hypothetical protein (NCBI) 91, 239
GSU2305 GSU2305 peptidoglycan-associated lipoprotein (VIMSS) 111, 143
GSU2306 purE-2 phosphoribosylaminoimidazole carboxylase, catalytic subunit (NCBI) 91, 111
GSU2307 GSU2307 carbonic anhydrase (NCBI) 91, 111
GSU2308 scfA malate oxidoreductase (NCBI) 91, 111
GSU2333 GSU2333 membrane protein, putative (VIMSS) 80, 111
GSU2335 GSU2335 universal stress protein family (VIMSS) 91, 111
GSU2425 GSU2425 O-acetyl-L-homoserine sulfhydrylase (NCBI) 9, 91
GSU2495 GSU2495 cytochrome c family protein (NCBI) 91, 292
GSU2496 GSU2496 hypothetical protein (VIMSS) 91, 258
GSU3157 GSU3157 hydrolase, alpha/beta fold family (VIMSS) 91, 111
GSU3191 GSU3191 TPR domain protein (VIMSS) 91, 111
GSU3378 GSU3378 glutamate-ammonia ligase adenylyltransferase domain protein (NCBI) 111, 208
GSU3379 GSU3379 translation initiation factor, putative, aIF-2BI family (VIMSS) 91, 111
GSU3380 gatB glutamyl-tRNA(Gln) amidotransferase, B subunit (NCBI) 91, 239
GSU3381 gatA glutamyl-tRNA(Gln) amidotransferase, A subunit (NCBI) 91, 111
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 GSU2306
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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