Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Functional Annotations (1)
|Aminoacyl-tRNA biosynthesis||kegg/ kegg pathway|
Regulation information for RSP_4345(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_4345
|Aminoacyl-tRNA biosynthesis||kegg/ kegg pathway|
Module neighborhood information for RSP_4345
|Gene||Common Name||Description||Module membership|
|RSP_0028||RSP_0028||Putative short-chain dehydrogenase/reductase (NCBI)||246, 251|
|RSP_0522||RSP_0522||putative oxidoreductase (NCBI)||217, 246|
|RSP_0835||manB||phosphomannomutase (NCBI)||153, 246|
|RSP_1115||RSP_1115||hypothetical protein (NCBI)||246, 292|
|RSP_1116||RSP_1116||glycosyltransferase (NCBI)||196, 246|
|RSP_1117||RSP_1117||hypothetical protein (NCBI)||137, 246|
|RSP_1118||RSP_1118||group 1 glycosyltransferase (NCBI)||246, 292|
|RSP_1119||RSP_1119||ABC protein exporter, fused ATPase and inner membrane subunits (NCBI)||196, 246|
|RSP_1120||RSP_1120||protein secretion protein, HlyD family, membrane fusion protein (NCBI)||137, 246|
|RSP_1284||prkA||Phosphoribulokinase (NCBI)||34, 284|
|RSP_1285||cbbF1||Fructose-1,6-bisphosphatase I (NCBI)||34, 284|
|RSP_1302||motB||putative chemotaxis MotB protein (NCBI)||31, 246|
|RSP_1303||flgE||putative flagellar hook protein (NCBI)||29, 246|
|RSP_1304||RSP_1304||putative flagellar hook protein (NCBI)||124, 246|
|RSP_1305||RSP_1305||putative flagellar hook-associated protein (NCBI)||138, 246|
|RSP_1307||flgI||putative flagellar P-ring protein (NCBI)||31, 246|
|RSP_1630||RSP_1630||hypothetical protein (NCBI)||31, 246|
|RSP_2757||RSP_2757||hypothetical protein (NCBI)||236, 246|
|RSP_2758||RSP_2758||hypothetical protein (NCBI)||246, 251|
|RSP_2759||RSP_2759||hypothetical protein (NCBI)||246, 282|
|RSP_2760||RSP_2760||hypothetical protein (NCBI)||246, 251|
|RSP_2761||RSP_2761||putative P2-like prophage tail protein X (NCBI)||246, 282|
|RSP_3108||RSP_3108||Putative methyl accepting chemotaxis protein (NCBI)||246, 292|
|RSP_3116||RSP_3116||Conserved hypothetical membrane/transport protein (NCBI)||246, 370|
|RSP_3266||fbpB||fructose-1,6-bisphosphatase (NCBI)||34, 284|
|RSP_3267||prkB||Phosphoribulokinase (NCBI)||34, 284|
|RSP_3268||tklB||Transketolase (NCBI)||34, 284|
|RSP_3269||gapB||Glyceraldehyde 3-phosphate dehydrogenase (NCBI)||34, 284|
|RSP_3270||cfxB||Fructose-bisphosphate aldolase II (NCBI)||34, 284|
|RSP_3271||rbpL||Ribulose bisphosphate carboxylase, large chain, form II (NCBI)||34, 284|
|RSP_3284||iolD||Acetolactate synthase (NCBI)||176, 246|
|RSP_3285||iolE||possible sugar phosphate isomerases/epimerases, IolE (NCBI)||150, 246|
|RSP_3286||iolB||Uncharacterized enzyme involved in inositol metabolism, IolB (NCBI)||246, 380|
|RSP_3630||RSP_3630||hypothetical protein (NCBI)||246, 253|
|RSP_3811||RSP_3811||hypothetical protein (NCBI)||138, 246|
|RSP_4326||RSP_4326||tRNA-Leu (NCBI)||34, 257|
|RSP_4345||RSP_4345||tRNA-Glu (NCBI)||34, 246|
|RSP_6081||RSP_6081||hypothetical protein (NCBI)||34, 284|
|RSP_6168||RSP_6168||ABC Cobalt transporter, periplasmic binding protein CbiN (NCBI)||34, 241|
|RSP_6189||RSP_6189||hypothetical protein (NCBI)||34, 230|
|RSP_6245||RSP_6245||hypothetical protein (NCBI)||8, 34|
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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- 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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