Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0889(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_0889
Module neighborhood information for RSP_0889
|Gene||Common Name||Description||Module membership|
|RSP_0015||RSP_0015||ABC spermidine/putrescine transporter, ATPase subunit (NCBI)||221, 358|
|RSP_0090||smoC||Operon regulator SmoC (NCBI)||99, 358|
|RSP_0223||RSP_0223||hypothetical protein (NCBI)||93, 358|
|RSP_0224||RSP_0224||ATP-dependent helicase (NCBI)||93, 358|
|RSP_0282||ppsR||Transcriptional regulator, PpsR (NCBI)||358, 381|
|RSP_0341||RSP_0341||Cytosine deaminase (NCBI)||57, 114|
|RSP_0342||RSP_0342||putative ABC sugar transporter, inner membrane subunit (NCBI)||57, 114|
|RSP_0343||RSP_0343||putative ABC sugar transporter, inner membrane subunit (NCBI)||57, 204|
|RSP_0344||RSP_0344||putative ABC sugar transporter, fused ATPase subunits (NCBI)||57, 204|
|RSP_0347||RSP_0347||ABC transporter, inner membrane subunit (NCBI)||57, 204|
|RSP_0348||RSP_0348||ABC transporter, inner membrane subunit (NCBI)||57, 204|
|RSP_0468||RSP_0468||putative 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (NCBI)||275, 358|
|RSP_0582||RSP_0582||possible penicillin binding protein (NCBI)||118, 358|
|RSP_0712||recR||recombination protein RecR (NCBI)||173, 358|
|RSP_0805||DppC||ABC dipeptide transporter, inner membrane subunit DppC (NCBI)||57, 67|
|RSP_0889||glnK||Nitrogen regulatory protein P-II (NCBI)||57, 358|
|RSP_1565||appA||AppA, antirepressor of ppsR, sensor of blue light (NCBI)||139, 358|
|RSP_1590||RSP_1590||two component, sigma54 specific, transcriptional regulator, fis family (NCBI)||175, 358|
|RSP_2042||RSP_2042||hypothetical protein (NCBI)||65, 358|
|RSP_2044||RSP_2044||ATPase (NCBI)||65, 358|
|RSP_2047||RSP_2047||ThiF family protein (NCBI)||100, 358|
|RSP_2048||RSP_2048||hypothetical protein (NCBI)||100, 358|
|RSP_2090||pycA||Pyruvate carboxylase (NCBI)||16, 57|
|RSP_2158||RSP_2158||ABC transporter, periplasmic solute-binding protein (NCBI)||57, 59|
|RSP_2210||RSP_2210||ABC sugar transporter, fused ATPase subunits (NCBI)||174, 358|
|RSP_2338||RSP_2338||hypothetical protein (NCBI)||358, 377|
|RSP_2415||RSP_2415||hypothetical protein (NCBI)||82, 358|
|RSP_2416||RSP_2416||hypothetical protein (NCBI)||82, 358|
|RSP_2417||RSP_2417||hypothetical protein (NCBI)||82, 358|
|RSP_3037||RSP_3037||Putative short-chain dehydrogenase/reductase (NCBI)||57, 168|
|RSP_3038||RSP_3038||ABC permidine/putrescine transporter, inner membrane subunit (NCBI)||57, 106|
|RSP_3039||RSP_3039||ABC permidine/putrescine transporter, inner membrane subunit (NCBI)||57, 106|
|RSP_3040||RSP_3040||ABC permidine/putrescine transporter, periplasmic substrate-binding protein (NCBI)||57, 106|
|RSP_3041||RSP_3041||ABC permidine/putrescine transporter, ATPase subunit (NCBI)||57, 106|
|RSP_3042||dorX||DMSO reductase regulatory protein DorX (NCBI)||57, 106|
|RSP_3215||RSP_3215||hypothetical protein (NCBI)||176, 358|
|RSP_3248||RSP_3248||ABC peptide transporter, periplasmic binding protein (NCBI)||57, 114|
|RSP_3381||RSP_3381||NAD(P)H -dependent quinone oxidoreductase (NCBI)||57, 175|
|RSP_3382||RSP_3382||hypothetical protein (NCBI)||57, 102|
|RSP_3383||RSP_3383||hypothetical protein (NCBI)||57, 102|
|RSP_3513||RSP_3513||GAF sensor diguanylate cyclase (NCBI)||57, 293|
|RSP_3687||RSP_3687||ABC sugar transporter, periplasmic binding protein (NCBI)||57, 171|
|RSP_3688||RSP_3688||ABC sugar transporter, ATPase subunit (NCBI)||57, 171|
|RSP_3689||yphD||ABC sugar transporter, inner membrane subunit (NCBI)||57, 88|
|RSP_3691||RSP_3691||putative cytoplasmic protein (NCBI)||31, 57|
|RSP_3750||RSP_3750||hypothetical protein (NCBI)||21, 358|
|RSP_3751||RSP_3751||hypothetical protein (NCBI)||21, 358|
|RSP_3752||RSP_3752||hypothetical protein (NCBI)||21, 358|
|RSP_3755||RSP_3755||hypothetical protein (NCBI)||21, 358|
|RSP_3756||RSP_3756||hypothetical protein (NCBI)||21, 358|
|RSP_3757||RSP_3757||hypothetical protein (NCBI)||21, 358|
|RSP_3758||RSP_3758||Cytosine-specific DNA methylase (NCBI)||57, 130|
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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