Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_2082(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_2082
Module neighborhood information for RSP_2082
|Gene||Common Name||Description||Module membership|
|RSP_0165||RSP_0165||hypothetical protein (NCBI)||58, 345|
|RSP_0193||RSP_0193||hypothetical protein (NCBI)||87, 372|
|RSP_0195||RSP_0195||NADH-ubiquinone oxidoreductase 17.2 kD subunit (NCBI)||87, 372|
|RSP_0247||RSP_0247||aminomethyltransferase related to GcvT (NCBI)||317, 372|
|RSP_0359||cbbI||Ribose-5-phosphate isomerase (NCBI)||127, 372|
|RSP_0418||RSP_0418||hypothetical protein (NCBI)||58, 234|
|RSP_0553||ruvB||Holiday junction DNA helicase RuvB (NCBI)||299, 372|
|RSP_0601||rpoH2||sigma factor RpoH2 (Sigma-32 group (NCBI)||58, 161|
|RSP_0611||RSP_0611||transcriptional regulator, ArsR family (NCBI)||58, 274|
|RSP_0705||RSP_0705||Cytochrome cy (NCBI)||58, 271|
|RSP_0882||DapA||Dihydrodipicolinate synthetase (NCBI)||182, 372|
|RSP_0899||RSP_0899||AhpC/TSA family protein (NCBI)||58, 142|
|RSP_1200||RSP_1200||putative membrane protein (NCBI)||152, 372|
|RSP_1343||RSP_1343||DNA polymerase III, beta chain (NCBI)||25, 372|
|RSP_1346||RSP_1346||DNA gyrase, subunit B (NCBI)||192, 372|
|RSP_1403||RSP_1403||conserved hypoothetical protein (NCBI)||58, 181|
|RSP_1490||RSP_1490||Putative ATP-dependent protease La, LON (NCBI)||231, 372|
|RSP_1511||RSP_1511||hypothetical protein (NCBI)||215, 372|
|RSP_1562||RSP_1562||fumarylacetoacetate hydrolase family protein (NCBI)||294, 372|
|RSP_1692||pduO||hypothetical protein (NCBI)||58, 231|
|RSP_1776||greA||Transcription elongation factor greA (NCBI)||240, 372|
|RSP_1833||RSP_1833||putative ribosomal-protein-alanine acetyltransferase (NCBI)||326, 372|
|RSP_1875||RSP_1875||hypothetical protein (NCBI)||345, 372|
|RSP_1947||cbbJ||Triosephosphate isomerase (NCBI)||278, 372|
|RSP_1969||purM||Phosphoribosylformylglycinamidine cyclo-ligase (NCBI)||258, 372|
|RSP_2009||argF||Aspartate/ornithine carbamoyltransferase (NCBI)||192, 372|
|RSP_2038||RSP_2038||possible acetyltransferase (NCBI)||213, 372|
|RSP_2082||RSP_2082||putative NADH-ubiquinone oxidoreductase-related protein (NCBI)||58, 372|
|RSP_2083||uvrB||Putative Excinuclease subunit B (NCBI)||152, 372|
|RSP_2128||purQ||phosphoribosylformylglycinamidine synthase I (FGAM) synthase (NCBI)||58, 231|
|RSP_2161||bcrC||Efflux channel (NCBI)||26, 58|
|RSP_2228||RSP_2228||PAS domain containing protein (NCBI)||58, 353|
|RSP_2229||RSP_2229||Chemotaxis multidomain, CheB methylesterase/CheR, Methylase (NCBI)||58, 353|
|RSP_2346||RSP_2346||Cold-shock DNA-binding domain protein (NCBI)||58, 274|
|RSP_2347||RSP_2347||hypothetical protein (NCBI)||58, 274|
|RSP_2519||RSP_2519||hypothetical protein (NCBI)||269, 372|
|RSP_2533||RSP_2533||Putative transcriptional regulator (NCBI)||361, 372|
|RSP_2538||fabG||Short-chain dehydrogenase/reductase (NCBI)||58, 274|
|RSP_2542||RSP_2542||ATPase (NCBI)||130, 372|
|RSP_2547||exoY||exopolysaccharide production protein exoY (NCBI)||58, 349|
|RSP_2548||exoF||Outer membrane polysaccharide export protein, exoF (NCBI)||58, 349|
|RSP_2647||RSP_2647||Predicted SAM-dependent methyltransferases (NCBI)||192, 372|
|RSP_2943||argS||Arginyl-tRNA synthetase, class I (NCBI)||160, 372|
|RSP_2961||RSP_2961||Protein containing a CBS domain (NCBI)||58, 274|
|RSP_2976||RSP_2976||hypothetical protein (NCBI)||58, 372|
|RSP_3162||RSP_3162||hypothetical protein (NCBI)||58, 231|
|RSP_3163||RSP_3163||Probable oxidoreductase (NCBI)||58, 231|
|RSP_3164||RSP_3164||ferredoxin like protein (NCBI)||58, 231|
|RSP_3179||fur||probable Ferric-uptake regulator (NCBI)||58, 363|
|RSP_3261||bioA||Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (BioA) (NCBI)||354, 372|
|RSP_3262||RSP_3262||Putative thioesterase (NCBI)||259, 372|
|RSP_3717||RSP_3717||hypothetical protein (NCBI)||17, 58|
|RSP_3718||RSP_3718||hypothetical protein (NCBI)||17, 58|
|RSP_3721||RSP_3721||hypothetical protein (NCBI)||58, 274|
|RSP_4315||RSP_4315||tRNA-Met (NCBI)||75, 372|
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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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.
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