Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_0444(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_0444
Module neighborhood information for RSP_0444
|Gene||Common Name||Description||Module membership|
|RSP_0189||RSP_0189||NADPH-dependent glutamate synthase beta chain and related oxidoreductase (NCBI)||43, 208|
|RSP_0190||accB||Biotin carboxyl carrier protein, AccB (NCBI)||43, 208|
|RSP_0191||accC||Biotin carboxylase (NCBI)||43, 208|
|RSP_0192||aat||possible leucyl/phenylalanyl-tRNA--protein transferase (NCBI)||43, 208|
|RSP_0367||RSP_0367||Preprotein translocase SecG subunit (NCBI)||203, 360|
|RSP_0381||RSP_0381||hypothetical protein (NCBI)||14, 43|
|RSP_0385||RSP_0385||Threonyl-tRNA synthetase, class IIa (NCBI)||166, 360|
|RSP_0444||RSP_0444||hypothetical protein (NCBI)||43, 360|
|RSP_0587||RSP_0587||Putative ABC transporter, fused ATPase subunits (NCBI)||109, 360|
|RSP_0842||RSP_0842||putative porin (NCBI)||43, 310|
|RSP_0887||MrcB||Glycosyl transferase, family 51 (NCBI)||43, 112|
|RSP_0929||accD||Acetyl-CoA carboxylase carboxyl transferase, beta subunit (NCBI)||309, 360|
|RSP_0971||RSP_0971||Putative membrane protein (NCBI)||43, 118|
|RSP_0972||RSP_0972||hypothetical protein (NCBI)||43, 118|
|RSP_1039||atpI||FoF1 ATP synthase, subunit I (NCBI)||43, 369|
|RSP_1064||RSP_1064||Putative preprotein translocase, YidC (NCBI)||43, 369|
|RSP_1157||PSrp1||Ribosomal subunit interface protein Y (NCBI)||43, 310|
|RSP_1169||secA||preprotein translocase, SecA subunit, ATPase (NCBI)||43, 277|
|RSP_1201||RSP_1201||hypothetical protein (NCBI)||43, 327|
|RSP_1231||rho||Transcription termination factor rho (NCBI)||43, 182|
|RSP_1351||serC||phosphoserine aminotransferase (NCBI)||85, 360|
|RSP_1352||RSP_1352||D-3-phosphoglycerate dehydrogenase (NCBI)||85, 360|
|RSP_1494||RSP_1494||putative aspartate aminotransferase (NCBI)||349, 360|
|RSP_1495||RSP_1495||Putative cell division protein (NCBI)||349, 360|
|RSP_1514||ahcY||Adenosylhomocysteinase (NCBI)||299, 360|
|RSP_1519||prrC||PrrC (NCBI)||43, 360|
|RSP_1667||RSP_1667||hypothetical protein (NCBI)||43, 112|
|RSP_1668||FolK||2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase (NCBI)||43, 112|
|RSP_1674||RSP_1674||type 1 signal peptidase (NCBI)||224, 360|
|RSP_1763||pheS||Phenylalanyl-tRNA synthetase alpha subunit (NCBI)||109, 360|
|RSP_1808||trpS||tryptophanyl-tRNA synthetase (NCBI)||71, 360|
|RSP_1851||metZ||O-succinylhomoserine sulfhydrylase (NCBI)||71, 360|
|RSP_1860||RSP_1860||hypothetical protein (NCBI)||43, 377|
|RSP_2126||purC||SAICAR synthetase (NCBI)||261, 360|
|RSP_2258||purC||SAICAR synthetase (NCBI)||43, 109|
|RSP_2425||RSP_2425||putative CarD-like transcriptional regulator (NCBI)||43, 112|
|RSP_2536||rhlE||ATP-dependent helicase, DEAD-box (NCBI)||43, 195|
|RSP_2543||RSP_2543||Peptidoglycan-binding LysM (possible peptidase) (NCBI)||261, 360|
|RSP_2630||gyrA||DNA gyrase/topoisomerase IV, subunit A (NCBI)||43, 182|
|RSP_2705||pyrH||Uridylate kinase (NCBI)||109, 360|
|RSP_2706||frr||Ribosome recycling factor (NCBI)||109, 360|
|RSP_2710||RSP_2710||Putative membrane-associated zinc metalloprotease (NCBI)||36, 360|
|RSP_2711||RSP_2711||putative outer membrane protein (NCBI)||43, 360|
|RSP_2956||tktA||Transketolase (NCBI)||166, 360|
|RSP_2959||gapB||Glyceraldehyde 3-phosphate dehydrogenase B (GAPDH) (NCBI)||184, 360|
|RSP_2974||RSP_2974||Putative metalopeptidase (NCBI)||43, 118|
|RSP_3177||fabB||3-oxoacyl-(Acyl-carrier-protein) synthase (NCBI)||360, 363|
|RSP_3178||fabA||3-hydroxydecanoyl-(acyl-carrier-protein) dehydratase (NCBI)||360, 363|
|RSP_3595||metK||S-adenosylmethionine synthetase (NCBI)||43, 85|
|RSP_4294||RSP_4294||16S ribosomal RNA (NCBI)||14, 43|
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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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.
Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.
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
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