Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_3653(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Module neighborhood information for RSP_3653
|Gene||Common Name||Description||Module membership|
|RSP_0543||fixU||hypothetical protein (NCBI)||141, 244|
|RSP_0544||nifZ||probable NifZ (NCBI)||141, 354|
|RSP_0545||RSP_0545||hypothetical protein (NCBI)||141, 300|
|RSP_0634||RSP_0634||TRAP-T family transporter, DctM (12 TMs) subunit (NCBI)||17, 141|
|RSP_0635||RSP_0635||TRAP-T family transporter, DctQ (4 TMs) subunit (NCBI)||17, 141|
|RSP_0636||RSP_0636||TRAP-T family transporter, DctP (periplasmic binding) subunit (NCBI)||17, 141|
|RSP_0700||RSP_0700||probable glycosyltransferase (NCBI)||233, 326|
|RSP_0701||RSP_0701||ABC peptide transporter, fused ATPase domains (NCBI)||233, 326|
|RSP_0838||RSP_0838||putative DNA polymerase III, delta subunit / DNA binding (NCBI)||141, 342|
|RSP_0888||amtB||Ammonium transporter, AmtB (NCBI)||141, 183|
|RSP_1042||RSP_1042||hypothetical protein (NCBI)||141, 357|
|RSP_1069||RSP_1069||hypothetical protein (NCBI)||233, 267|
|RSP_1392||thiP||ABC thiamine transporter, inner membrane subunit (NCBI)||233, 234|
|RSP_1433||RSP_1433||hypothetical protein (NCBI)||141, 285|
|RSP_1441||RSP_1441||regulatory protein, GntR family (NCBI)||89, 141|
|RSP_1616||RSP_1616||hypothetical protein (NCBI)||141, 342|
|RSP_1638||RSP_1638||hypothetical protein (NCBI)||233, 236|
|RSP_1639||RSP_1639||hypothetical protein (NCBI)||233, 253|
|RSP_1640||RSP_1640||hypothetical protein (NCBI)||168, 233|
|RSP_1641||RSP_1641||hypothetical protein (NCBI)||233, 300|
|RSP_1644||RSP_1644||hypothetical protein (NCBI)||233, 300|
|RSP_1645||RSP_1645||putative phage-related protein (NCBI)||191, 233|
|RSP_1646||RSP_1646||possible transmembrane protein (NCBI)||233, 308|
|RSP_1652||RSP_1652||hypothetical protein (NCBI)||73, 141|
|RSP_1694||RSP_1694||Probable short-chain dehydrogenase/reductase (NCBI)||233, 304|
|RSP_1782||RSP_1782||hypothetical membrane protein (NCBI)||233, 235|
|RSP_1783||RSP_1783||Predicted membrane protein (NCBI)||233, 235|
|RSP_1900||RSP_1900||hypothetical protein (NCBI)||91, 233|
|RSP_2010||RSP_2010||hypothetical protein (NCBI)||141, 343|
|RSP_2553||RSP_2553||hypothetical protein (NCBI)||141, 157|
|RSP_2677||RSP_2677||Putative Mg++ transport associated protein, MgtC (NCBI)||138, 141|
|RSP_2756||RSP_2756||hypothetical protein (NCBI)||125, 141|
|RSP_2874||RSP_2874||Putative Beta-glucosidase A (NCBI)||229, 233|
|RSP_2884||glgX||glycogen debranching enzyme (NCBI)||233, 340|
|RSP_3025||RSP_3025||possible NAD(P)H oxidoreductase (NCBI)||141, 303|
|RSP_3036||RSP_3036||hypothetical protein (NCBI)||38, 141|
|RSP_3060||cysE||possible O-acetylserine synthase (NCBI)||141, 370|
|RSP_3061||RSP_3061||hypothetical protein (NCBI)||38, 141|
|RSP_3062||fabG||3-oxoacyl-(acyl-carrier-protein) reductase (NCBI)||141, 370|
|RSP_3122||RSP_3122||putative Glutathione S-transferase (NCBI)||233, 249|
|RSP_3137||RSP_3137||hypothetical protein (NCBI)||141, 168|
|RSP_3287||upgC||ABC glycerol-3-phosphate transporter, ATPase subunit UpgC (NCBI)||115, 233|
|RSP_3288||ugpE||ABC glycerol-3-phosphate transporter, inner membrane subunit UgpE (NCBI)||115, 233|
|RSP_3289||ugpA||ABC glycerol-3-phosphate transporter, inner membrane subunit UgpA (NCBI)||115, 233|
|RSP_3290||ugpB||ABC glycerol-3-phosphate transporter, periplasmic binding protein, UgpB (NCBI)||115, 233|
|RSP_3335||RSP_3335||ABC spermidine/putrescine transporter, inner membrane subunit (NCBI)||44, 141|
|RSP_3336||RSP_3336||ABC spermidine/putrescine transporter, inner membrane subunit (NCBI)||44, 141|
|RSP_3443||RSP_3443||putative acetamidase/formamidase (NCBI)||61, 141|
|RSP_3651||RSP_3651||putative membrane protein (NCBI)||189, 233|
|RSP_3652||RSP_3652||Predicted phage phi-C31 gp36 major capsid-like protein (NCBI)||141, 233|
|RSP_3653||RSP_3653||hypothetical protein (NCBI)||141, 233|
|RSP_3663||RSP_3663||TRAP-T family transporter, small (4TMs) inner membrane subunit (NCBI)||141, 342|
|RSP_3693||RSP_3693||BtpA protein (NCBI)||94, 233|
|RSP_3694||RSP_3694||Putative transcription activator (NCBI)||94, 233|
|RSP_3786||RSP_3786||hypothetical protein (NCBI)||141, 236|
|RSP_3788||RSP_3788||hypothetical protein (NCBI)||77, 233|
|RSP_3794||RSP_3794||hypothetical protein (NCBI)||29, 141|
|RSP_3797||RSP_3797||hypothetical protein (NCBI)||141, 157|
Gene Page Help
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.
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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.
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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.
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.
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CircVisOur 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
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