Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
hypothetical protein (NCBI)
Functional Annotations (2)
|nucleic acid binding||go/ molecular_function|
|endonuclease activity||go/ molecular_function|
Regulation information for RSP_1652(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|
Functional Enrichment for RSP_1652
|nucleic acid binding||go/ molecular_function|
|endonuclease activity||go/ molecular_function|
Module neighborhood information for RSP_1652
|Gene||Common Name||Description||Module membership|
|RSP_0088||RSP_0088||ycfI, putative structural proteins (NCBI)||73, 168|
|RSP_0133||RSP_0133||Na+/H+ antiporter, NhaC family (NCBI)||73, 196|
|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_0564||RSP_0564||hypothetical protein (NCBI)||19, 73|
|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_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_1210||RSP_1210||Response regulator receiver protein (NCBI)||73, 168|
|RSP_1319||RSP_1319||possible invasion protein (NCBI)||73, 238|
|RSP_1428||RSP_1428||Possible Pre (Mob) type recombination enzyme (NCBI)||73, 236|
|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_1652||RSP_1652||hypothetical protein (NCBI)||73, 141|
|RSP_2010||RSP_2010||hypothetical protein (NCBI)||141, 343|
|RSP_2052||RSP_2052||N6 adenine-specific DNA methyltransferase, D12 class (NCBI)||73, 379|
|RSP_2053||RSP_2053||Possible transporter, RarD family, DMT superfamily (NCBI)||73, 97|
|RSP_2123||RSP_2123||Radical SAM domain protein (NCBI)||73, 244|
|RSP_2220||RSP_2220||possible flagellar motor switch protein (fliG) (NCBI)||73, 196|
|RSP_2383||RSP_2383||putative integral membrane protein (NCBI)||73, 150|
|RSP_2553||RSP_2553||hypothetical protein (NCBI)||141, 157|
|RSP_2571||RSP_2571||putative oxidoreductase protein (NCBI)||73, 188|
|RSP_2675||RSP_2675||hypothetical protein (NCBI)||73, 189|
|RSP_2676||RSP_2676||hypothetical protein (NCBI)||73, 362|
|RSP_2677||RSP_2677||Putative Mg++ transport associated protein, MgtC (NCBI)||138, 141|
|RSP_2756||RSP_2756||hypothetical protein (NCBI)||125, 141|
|RSP_2766||RSP_2766||Uncharacterized metal-binding protein (NCBI)||73, 124|
|RSP_2770||RSP_2770||hypothetical protein (NCBI)||73, 238|
|RSP_2813||mttB||putative trimethylamine methyltransferase protein (NCBI)||73, 304|
|RSP_2873||aglE||ABC alpha-glucoside transporter, perplasmic substrate-binding protein (NCBI)||73, 307|
|RSP_3024||RSP_3024||transcriptional regulator, IclR family/MhpR (NCBI)||68, 73|
|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_3137||RSP_3137||hypothetical protein (NCBI)||141, 168|
|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_3542||RSP_3542||hypothetical protein (NCBI)||73, 189|
|RSP_3627||RSP_3627||Periplasmic serine proteases (NCBI)||73, 379|
|RSP_3631||RSP_3631||hypothetical protein (NCBI)||73, 253|
|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_3786||RSP_3786||hypothetical protein (NCBI)||141, 236|
|RSP_3793||RSP_3793||hypothetical protein (NCBI)||73, 168|
|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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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.
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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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