Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1566(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_1566
Module neighborhood information for RSP_1566
|Gene||Common Name||Description||Module membership|
|RSP_0113||RSP_0113||Phospholipase D/Transphosphatidylase (NCBI)||176, 362|
|RSP_0114||RSP_0114||hypothetical protein (NCBI)||176, 294|
|RSP_0282||ppsR||Transcriptional regulator, PpsR (NCBI)||358, 381|
|RSP_0384||RSP_0384||hypothetical protein (NCBI)||329, 381|
|RSP_0415||RSP_0415||sigma-24 (NCBI)||308, 381|
|RSP_0429||RSP_0429||Probable ABC drug/toxin efflux transporter; fused ATPase and inner membrane subunits (NCBI)||176, 329|
|RSP_0511||RSP_0511||two component transcriptional regulator, LuxR family (NCBI)||168, 176|
|RSP_0599||RSP_0599||Probable DNA/pantothenate metabolism flavoprotein (NCBI)||242, 381|
|RSP_0708||RSP_0708||NUDIX hydrolase (NCBI)||242, 381|
|RSP_0710||dnaX||DNA polymerase III tau and gamma subunits (NCBI)||173, 381|
|RSP_0765||RSP_0765||SAM-dependent methyltransferase (NCBI)||10, 176|
|RSP_0941||RSP_0941||ABC transporter, ATPase subunit (NCBI)||92, 176|
|RSP_0942||RSP_0942||ABC transporter, inner membrane subunit (NCBI)||92, 176|
|RSP_1188||wcaG||Nucleotide sugar epimerase/dehydratase (NCBI)||59, 381|
|RSP_1214||RSP_1214||putative branched-chain amino acid aminotransferase (NCBI)||215, 381|
|RSP_1215||ilvE||putative IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase (NCBI)||68, 381|
|RSP_1342||dnaA||chromosomal replication initiator protein, DnaA (NCBI)||25, 381|
|RSP_1404||RSP_1404||Orotidine 5'-phosphate decarboxylase (NCBI)||311, 381|
|RSP_1405||RSP_1405||ROK family protein (NCBI)||285, 381|
|RSP_1520||prrB||Sensor histidine kinase PrrB (RegB) (NCBI)||16, 381|
|RSP_1524||RSP_1524||Nucleotidyltransferase family protein (NCBI)||110, 176|
|RSP_1553||RSP_1553||Probable glyoxylate induced protein (NCBI)||102, 381|
|RSP_1554||RSP_1554||Possible polysaccharide deacetylase (NCBI)||102, 381|
|RSP_1555||RSP_1555||Transthyretin-like protein (NCBI)||329, 381|
|RSP_1566||RSP_1566||hypothetical protein (NCBI)||176, 381|
|RSP_1600||RSP_1600||possible transporter, DME family, DMT superfamily (NCBI)||176, 350|
|RSP_1621||RSP_1621||Deoxyguanosinetriphosphate triphosphohydrolase-like protein (NCBI)||93, 381|
|RSP_1894||RSP_1894||hypothetical protein (NCBI)||323, 381|
|RSP_1908||RSP_1908||outer membrane protein, OmpA/MotB family (NCBI)||72, 381|
|RSP_1909||RSP_1909||Outer membrane general secretion pathway protein, Secretin (NCBI)||221, 381|
|RSP_1922||RSP_1922||Transcriptional regulator, GntR family, with aminotransferase domain (NCBI)||1, 176|
|RSP_1946||RSP_1946||Cytochrome P450 hydroxylase (NCBI)||175, 381|
|RSP_2003||yibQ||YibQ protein (NCBI)||176, 285|
|RSP_2026||RSP_2026||transcriptional regulator, AraC family (NCBI)||103, 176|
|RSP_2119||RSP_2119||hypothetical protein (NCBI)||10, 381|
|RSP_2160||gno||Short-chain dehydrogenase/reductase (NCBI)||20, 176|
|RSP_2694||RSP_2694||hypothetical protein (NCBI)||357, 381|
|RSP_2869||RSP_2869||Possible tellurite resistance protein (NCBI)||329, 381|
|RSP_2882||RSP_2882||two component transcriptional regulator, LuxR family (NCBI)||62, 381|
|RSP_2942||RSP_2942||hypothetical protein (NCBI)||349, 381|
|RSP_3052||RSP_3052||transcriptional regulator, LysR family (NCBI)||97, 176|
|RSP_3053||RSP_3053||Possible dioxygenase/glyoxalase family protein (NCBI)||97, 176|
|RSP_3055||RSP_3055||transcriptional regulator, MarR family (NCBI)||176, 242|
|RSP_3085||RSP_3085||Conserved hypothetical membrane protein (NCBI)||157, 176|
|RSP_3086||RSP_3086||periplasmic sensor signal transduction histidine kinase (NCBI)||83, 176|
|RSP_3087||dgkA||diacylglycerol kinase (NCBI)||97, 176|
|RSP_3088||RSP_3088||two component transcriptional regulator, winged helix family (NCBI)||176, 213|
|RSP_3157||RSP_3157||ABC transporter, inner membrane subunit (NCBI)||19, 176|
|RSP_3202||RSP_3202||transcriptional regulator, AraC family (NCBI)||82, 176|
|RSP_3215||RSP_3215||hypothetical protein (NCBI)||176, 358|
|RSP_3226||RSP_3226||Silent information regulator protein, Sir2 (NCBI)||99, 381|
|RSP_3245||RSP_3245||Possible transporter, Major facilitator superfamily (MFS) (NCBI)||176, 380|
|RSP_3284||iolD||Acetolactate synthase (NCBI)||176, 246|
|RSP_3376||aroQ||3 dehydroquinase dehydratase, class II (NCBI)||240, 381|
|RSP_3377||RSP_3377||Glutathione S-transferase family protein (NCBI)||176, 216|
|RSP_3419||RSP_3419||hypothetical protein (NCBI)||175, 381|
|RSP_3466||RSP_3466||hypothetical protein (NCBI)||147, 176|
|RSP_3467||RSP_3467||hypothetical protein (NCBI)||147, 176|
|RSP_3468||RSP_3468||hypothetical protein (NCBI)||147, 176|
|RSP_3469||RSP_3469||hypothetical protein (NCBI)||147, 176|
|RSP_3470||RSP_3470||hypothetical protein (NCBI)||147, 176|
|RSP_3507||RSP_3507||hypothetical protein (NCBI)||381, 384|
|RSP_3553||dnaE||DNA polymerase III alpha chain (NCBI)||291, 381|
|RSP_3629||RSP_3629||hypothetical protein (NCBI)||176, 302|
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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Module Members Tab
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
- 3. Target genes (other module members)
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- 5. Module(s) that source gene and target genes belong to
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