Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1006(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_1006
|Gene||Common Name||Description||Module membership|
|RSP_0419||RSP_0419||hypothetical protein (NCBI)||10, 308|
|RSP_0586||RSP_0586||probable nicotinate-nucleotide adenylyltransferase (NCBI)||7, 215|
|RSP_0650||RSP_0650||Probable transglycosylase (NCBI)||7, 33|
|RSP_0674||RSP_0674||Putative HolB DNA polymerase III delta prime subunit (NCBI)||10, 36|
|RSP_0715||RSP_0715||Ribonuclease T2 (NCBI)||10, 35|
|RSP_0765||RSP_0765||SAM-dependent methyltransferase (NCBI)||10, 176|
|RSP_0766||RSP_0766||hypothetical protein (NCBI)||10, 56|
|RSP_0825||ppnk||probable inorganic polyphosphate/ATP-NAD kinase (NCBI)||1, 10|
|RSP_0845||RSP_0845||hypothetical protein (NCBI)||4, 10|
|RSP_0846||ribA||GTP cyclohydrolase II (NCBI)||4, 10|
|RSP_0847||RSP_0847||two component transcriptional regulator, winged helix family (NCBI)||10, 287|
|RSP_0866||RSP_0866||hypothetical protein (NCBI)||7, 357|
|RSP_0879||RSP_0879||hypothetical protein (NCBI)||7, 65|
|RSP_0895||RSP_0895||phosphodiesterase-like (NCBI)||7, 175|
|RSP_0896||RSP_0896||hypothetical protein (NCBI)||7, 87|
|RSP_0897||RSP_0897||Glutathione S-transferase (NCBI)||10, 20|
|RSP_0949||ostB||putative trehalose-6-phosphate phosphatase (NCBI)||7, 368|
|RSP_1005||gshA||putative glutathione synthetase (NCBI)||7, 181|
|RSP_1006||RSP_1006||hypothetical protein (NCBI)||7, 10|
|RSP_1007||RSP_1007||hypothetical protein (NCBI)||10, 127|
|RSP_1187||RSP_1187||hypothetical protein (NCBI)||7, 59|
|RSP_1219||grpE||putative chaperone protein GrpE (heat shock protein) (NCBI)||7, 187|
|RSP_1220||hrcA||heat-inducible transcription repressor HrcA (NCBI)||10, 216|
|RSP_1223||tdcF||Putative translation initiation inhibitor, yjgF family / putative Endoribonuclease L-PSP (NCBI)||7, 258|
|RSP_1337||aarF||probable ubiquinone biosynthesis protein (NCBI)||7, 108|
|RSP_1380||RSP_1380||hypothetical protein (NCBI)||7, 175|
|RSP_1384||RSP_1384||hypothetical protein (NCBI)||10, 323|
|RSP_1387||RSP_1387||AMP nucleosidase (NCBI)||7, 308|
|RSP_1468||RSP_1468||Site-specific DNA-methyltransferase (NCBI)||7, 218|
|RSP_1570||purK||Phosphoribosylaminoimidazole carboxylase, ATPase subunit (NCBI)||7, 374|
|RSP_1775||RSP_1775||hypothetical protein (NCBI)||7, 240|
|RSP_1794||RSP_1794||putative lytic transglycosylase (NCBI)||10, 250|
|RSP_1834||RSP_1834||hypothetical protein (NCBI)||10, 185|
|RSP_1868||RSP_1868||serine-pyruvate aminotransferase (NCBI)||10, 127|
|RSP_1891||RSP_1891||Zinc-binding dehydrogenase (NCBI)||10, 158|
|RSP_2104||RSP_2104||hypothetical protein (NCBI)||7, 298|
|RSP_2119||RSP_2119||hypothetical protein (NCBI)||10, 381|
|RSP_2120||RSP_2120||putative D-lactate dehydrogenase (cytochrome), FAD/FMN-containing oxidoreductase (NCBI)||10, 127|
|RSP_2142||RSP_2142||NifS-related protein (NCBI)||4, 10|
|RSP_2282||chrA||Chromate efflux pump, ChrA (NCBI)||10, 107|
|RSP_2505||creA||possible CreA protein (NCBI)||10, 237|
|RSP_2544||RSP_2544||Protein-L-isoaspartate O-methyltransferase (NCBI)||7, 72|
|RSP_2551||exoO||Glycosyl transferase, family 2 (NCBI)||10, 100|
|RSP_2618||RSP_2618||Putative hemolysin (NCBI)||10, 341|
|RSP_2651||RSP_2651||hypothetical protein (NCBI)||7, 110|
|RSP_2652||RSP_2652||putative Acetyltransferase (NCBI)||7, 110|
|RSP_2715||RSP_2715||hypothetical protein (NCBI)||7, 114|
|RSP_2716||lpxB||putative lipid-A-disaccharide synthase (NCBI)||7, 240|
|RSP_2825||cobK||Putative precorrin-6x reductase (NCBI)||1, 10|
|RSP_2917||RSP_2917||putative cystathionine gamma-synthase beta-lyase (NCBI)||7, 383|
|RSP_2950||RSP_2950||Transcriptional regulator, LysR family (NCBI)||7, 263|
|RSP_3209||cbiQ||ABC cobalt transporter, inner membrane subunit, CbiQ (NCBI)||7, 100|
|RSP_3237||lguL||Lactoylglutathione lyase (NCBI)||7, 301|
|RSP_3564||RSP_3564||Generic methyltransferase (NCBI)||7, 215|
|RSP_3606||RSP_3606||Sigma54-2 (RNA polymerase sigma-54 factor) (NCBI)||10, 162|
|RSP_3836||RSP_3836||Putative metal-dependent hydrolase (NCBI)||10, 329|
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.
- 2. Source gene
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