Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
hypothetical protein (NCBI)
Functional Annotations (1)
Regulation information for RSP_0135(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_0135
Module neighborhood information for RSP_0135
|Gene||Common Name||Description||Module membership|
|RSP_0010||RSP_0010||homoserine O-succinyltransferase (NCBI)||91, 133|
|RSP_0135||RSP_0135||hypothetical protein (NCBI)||29, 133|
|RSP_0136||RSP_0136||putative integrase for prophage CP-933U (NCBI)||29, 140|
|RSP_0201||RSP_0201||ABC transporter, fused inner membrane subunits (NCBI)||121, 133|
|RSP_0307||RSP_0307||Antifreeze protein, type I (NCBI)||133, 265|
|RSP_0492||hupU||hydrogenase small subunit (NCBI)||83, 133|
|RSP_0604||RSP_0604||hypothetical protein (NCBI)||29, 249|
|RSP_0813||RSP_0813||Response regulator receiver protein (NCBI)||29, 157|
|RSP_0877||RSP_0877||Putative transporter, RhaT family, DMT superfamily (NCBI)||29, 187|
|RSP_0950||RSP_0950||Arginine utilization protein RocB (NCBI)||23, 133|
|RSP_1121||RSP_1121||acetyl transferase, Isoleucine patch superfamily (NCBI)||133, 242|
|RSP_1226||RSP_1226||hypothetical protein (NCBI)||133, 187|
|RSP_1303||flgE||putative flagellar hook protein (NCBI)||29, 246|
|RSP_1366||RSP_1366||Class I peptide chain release factor (NCBI)||53, 133|
|RSP_1400||RSP_1400||DNA polymerase IV (RefSeq)||11, 133|
|RSP_1417||RSP_1417||hypothetical protein (NCBI)||23, 133|
|RSP_1500||RSP_1500||possible anti-sigma regulatory kinase (NCBI)||29, 304|
|RSP_1502||RSP_1502||GAF domain protein (NCBI)||29, 174|
|RSP_1846||RSP_1846||hypothetical protein (NCBI)||133, 164|
|RSP_1853||TrkH2||potassium uptake transporter, transmembrane component, TrkH (NCBI)||29, 67|
|RSP_1967||RSP_1967||hypothetical protein (NCBI)||11, 133|
|RSP_2025||RSP_2025||hypothetical protein (NCBI)||29, 288|
|RSP_2079||RSP_2079||hypothetical protein (NCBI)||29, 380|
|RSP_2381||RSP_2381||putative 3-methyladenine DNA glycosylase (NCBI)||29, 101|
|RSP_2420||RSP_2420||hypothetical protein (NCBI)||82, 133|
|RSP_2476||RSP_2476||hypothetical protein (NCBI)||29, 110|
|RSP_2747||RSP_2747||possible glycosyltransferase (NCBI)||133, 335|
|RSP_3015||RSP_3015||hypothetical protein (NCBI)||29, 183|
|RSP_3084||RSP_3084||hypothetical protein (NCBI)||133, 183|
|RSP_3140||RSP_3140||hypothetical protein (NCBI)||133, 158|
|RSP_3308||RSP_3308||possible transporter, DME family, DMT superfamily (NCBI)||133, 375|
|RSP_3329||RSP_3329||hypothetical protein (NCBI)||133, 331|
|RSP_3340||rarD||possible transporter, RarD, DMT superfamily (NCBI)||133, 308|
|RSP_3349||RSP_3349||hypothetical protein (NCBI)||133, 166|
|RSP_3375||RSP_3375||Membrane fusion protein, HlyD family (NCBI)||22, 133|
|RSP_3379||RSP_3379||hypothetical protein (NCBI)||133, 146|
|RSP_3387||RSP_3387||TRAP-T family transporter, fused small and large inner membrane subunits (NCBI)||133, 220|
|RSP_3619||RSP_3619||hypothetical protein (NCBI)||133, 188|
|RSP_3777||RSP_3777||hypothetical protein (NCBI)||29, 356|
|RSP_3783||RSP_3783||putative bacteriophage-related protein, Phage portal protein, lambda family (NCBI)||29, 183|
|RSP_3794||RSP_3794||hypothetical protein (NCBI)||29, 141|
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
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