Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2755(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_2755
|Gene||Common Name||Description||Module membership|
|RSP_0118||RSP_0118||Cytochrome c oxidase, subunit IIc (NCBI)||77, 229|
|RSP_0151||RSP_0151||hypothetical protein (NCBI)||38, 74|
|RSP_0152||RSP_0152||P-loop ATPase (NCBI)||74, 280|
|RSP_0211||RSP_0211||hypothetical protein (NCBI)||74, 191|
|RSP_0212||RSP_0212||HNH nuclease (NCBI)||74, 193|
|RSP_0330||RSP_0330||hypothetical protein (NCBI)||74, 116|
|RSP_0524||RSP_0524||hypothetical protein (NCBI)||74, 168|
|RSP_0607||RSP_0607||sigma 24 (NCBI)||77, 103|
|RSP_0946||RSP_0946||putative DNA topoisomerase I protein (NCBI)||74, 150|
|RSP_1113||RSP_1113||Hemolysin-type calcium-binding region; RTX toxin (NCBI)||74, 115|
|RSP_1195||comF||Competence protein F (NCBI)||74, 150|
|RSP_1357||RSP_1357||cytoplasmic sensor hybrid histidine kinase (NCBI)||74, 137|
|RSP_1501||RSP_1501||Antisigma-factor antagonist (STAS) domain protein (NCBI)||74, 292|
|RSP_1602||RSP_1602||TRAP-T family transporter, DctM (12TMs) subunit (NCBI)||32, 77|
|RSP_1604||RSP_1604||TRAP-T family transporter, DctQ (4TMs) subunit (NCBI)||32, 77|
|RSP_1605||RSP_1605||TRAP-T family transporter, periplasmic binding protein, DctP (NCBI)||32, 77|
|RSP_1607||RSP_1607||Putative regulatory protein, GntR family (NCBI)||77, 214|
|RSP_1636||RSP_1636||phage-related protein, probable phage tail tape meausure protein, lambda family (NCBI)||31, 77|
|RSP_2070||RSP_2070||Putative Phage-related terminase (NCBI)||77, 304|
|RSP_2071||RSP_2071||hypothetical protein (NCBI)||77, 304|
|RSP_2182||betI||transcriptional regulator, BetI (NCBI)||77, 303|
|RSP_2183||betB||Betaine aldehyde dehydrogenase (NCBI)||77, 303|
|RSP_2184||betA||Choline dehydrogenase (NCBI)||77, 303|
|RSP_2351||RSP_2351||hypothetical protein (NCBI)||74, 362|
|RSP_2352||RSP_2352||putative terminase large subunit / phage terminase (NCBI)||74, 83|
|RSP_2353||RSP_2353||hypothetical protein (NCBI)||74, 83|
|RSP_2497||RSP_2497||ATPase (NCBI)||74, 238|
|RSP_2555||RSP_2555||hypothetical protein (NCBI)||77, 157|
|RSP_2556||RSP_2556||hypothetical protein (NCBI)||77, 157|
|RSP_2679||RSP_2679||ATP-dependent DNA ligase (NCBI)||74, 191|
|RSP_2750||RSP_2750||hypothetical protein (NCBI)||77, 105|
|RSP_2753||RSP_2753||hypothetical protein (NCBI)||77, 105|
|RSP_2755||RSP_2755||hypothetical protein (NCBI)||74, 77|
|RSP_2792||RSP_2792||putative monooxygenase alpha subunit (NCBI)||77, 103|
|RSP_2796||RSP_2796||hypothetical protein (NCBI)||77, 103|
|RSP_2798||groEL3||Putative chaperonin groEL (NCBI)||77, 103|
|RSP_2944||RSP_2944||hypothetical protein (NCBI)||77, 153|
|RSP_2995||RSP_2995||possible phage major capsid protein, gp36 (NCBI)||77, 153|
|RSP_3012||RSP_3012||Probable transposase (NCBI)||77, 126|
|RSP_3063||RSP_3063||AMP-dependent synthetase and ligase (NCBI)||74, 137|
|RSP_3065||RSP_3065||Putative transporter, Major facilitator superfamily (MFS) (NCBI)||77, 320|
|RSP_3114||RSP_3114||hypothetical protein (NCBI)||77, 282|
|RSP_3206||RSP_3206||Putative xanthine dehydrogenase (NCBI)||74, 236|
|RSP_3259||RSP_3259||Transcription antitermination protein (NCBI)||77, 236|
|RSP_3353||RSP_3353||Phage related tail protein (NCBI)||74, 150|
|RSP_3380||RSP_3380||hypothetical protein (NCBI)||77, 236|
|RSP_3393||RSP_3393||ABC opine/polyamine transporter, inner membrane subunit (NCBI)||77, 88|
|RSP_3414||RSP_3414||ABC Fe+3-siderophore transporter, inner membrane subunit (NCBI)||74, 196|
|RSP_3415||RSP_3415||ABC Fe+3-siderophore transporter, inner membrane subunit (NCBI)||74, 138|
|RSP_3416||RSP_3416||ABC Fe+3-siderophore transporter, periplasmic binding protein (NCBI)||74, 331|
|RSP_3420||RSP_3420||Methyl-accepting chemotaxis protein (NCBI)||77, 251|
|RSP_3421||RSP_3421||hypothetical protein (NCBI)||77, 105|
|RSP_3605||RSP_3605||FAD-dependent pyridine nucleotide-disulphide oxidoreductase (NCBI)||77, 273|
|RSP_3682||RSP_3682||hypothetical protein (NCBI)||74, 304|
|RSP_3788||RSP_3788||hypothetical protein (NCBI)||77, 233|
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.
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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
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