Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
conserved hypothetical protein (possibly transmembrane) (NCBI)
Functional Annotations (1)
Regulation information for RSP_1022(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_1022
Module neighborhood information for RSP_1022
|Gene||Common Name||Description||Module membership|
|RSP_0008||RSP_0008||possible transporter, DME family, DMT superfamily (NCBI)||323, 340|
|RSP_0214||RSP_0214||possible uncharacterized phage protein (NCBI)||323, 325|
|RSP_0382||RSP_0382||poly-beta-hydroxybutyrate polymerase (NCBI)||118, 200|
|RSP_0383||RSP_0383||hypothetical protein (NCBI)||200, 204|
|RSP_0393||RSP_0393||probable riboflavin biosynthesis protein (NCBI)||107, 323|
|RSP_0394||RSP_0394||hypothetical protein (NCBI)||200, 349|
|RSP_0563||RSP_0563||putative site-specific recombinase (NCBI)||220, 323|
|RSP_0600||RSP_0600||hypothetical protein (NCBI)||200, 350|
|RSP_0688||RSP_0688||Probable penicillin-binding protein (NCBI)||52, 200|
|RSP_0698||fnrL||Crp-Fnr regulatory protein (FnrL) (NCBI)||200, 262|
|RSP_0824||pth||Peptidyl-tRNA hydrolase (NCBI)||142, 323|
|RSP_0953||RSP_0953||hypothetical protein (NCBI)||121, 323|
|RSP_0959||RSP_0959||ATPase (NCBI)||174, 200|
|RSP_1022||RSP_1022||conserved hypothetical protein (possibly transmembrane) (NCBI)||200, 323|
|RSP_1023||RSP_1023||hypothetical protein (NCBI)||185, 200|
|RSP_1024||RSP_1024||Putative MoxR family protein (NCBI)||171, 200|
|RSP_1029||RSP_1029||possible Histidine triad (HIT) protein (NCBI)||127, 200|
|RSP_1109||cysK||Cysteine synthase (NCBI)||112, 200|
|RSP_1174||pip||Prolyl aminopeptidase (NCBI)||35, 323|
|RSP_1199||RSP_1199||secreted conserved hypothetical protein (NCBI)||200, 262|
|RSP_1365||RSP_1365||hypothetical protein (NCBI)||182, 323|
|RSP_1384||RSP_1384||hypothetical protein (NCBI)||10, 323|
|RSP_1474||nspC||putative carboxynorspermidine decarboxylase protein (NCBI)||271, 323|
|RSP_1780||RSP_1780||hypothetical protein (NCBI)||285, 323|
|RSP_1894||RSP_1894||hypothetical protein (NCBI)||323, 381|
|RSP_1924||RSP_1924||BioY family protein (NCBI)||296, 323|
|RSP_1993||RSP_1993||hypothetical protein (NCBI)||37, 323|
|RSP_2005||ybaU||possible peptidyl-prolyl cis-trans isomerse (NCBI)||203, 323|
|RSP_2018||RSP_2018||hypothetical protein (NCBI)||308, 323|
|RSP_2215||RSP_2215||hypothetical protein (NCBI)||223, 323|
|RSP_2261||ydjI||Antifreeze protein, type I (NCBI)||64, 200|
|RSP_2344||fabI1||enoyl-acyl carrier protein reductase (NCBI)||72, 200|
|RSP_2410||rpoH1||sigma factor RpoH1 (Sigma-32 group, heat shock) (NCBI)||200, 287|
|RSP_2550||exoK||endo-beta-1,3-1,4-glycanase protein (NCBI)||200, 262|
|RSP_2557||asnB||putative asparagine synthetase (NCBI)||157, 323|
|RSP_2561||exoP||putative succinoglycan biosynthesis transport protein ExoP (NCBI)||114, 200|
|RSP_2562||exoM||succinoglycan biosynthesis protein exoM (NCBI)||114, 200|
|RSP_2563||exoA||Glycosyl transferase, family 2 (NCBI)||114, 200|
|RSP_2564||exoL||glycosyltransferase, Succinoglycan biosynthesis protein exoL (NCBI)||114, 200|
|RSP_2565||ugpG||UDPG-pyrophosphorylase (NCBI)||200, 223|
|RSP_2639||RSP_2639||Putative arginine-tRNA protein transferase (NCBI)||46, 200|
|RSP_2746||RSP_2746||hypothetical protein (NCBI)||323, 335|
|RSP_2806||lon||Probable ATP-dependent protease La protein (NCBI)||3, 200|
|RSP_2946||argC||N-acetyl-gamma-glutamyl-phosphate reductase (NCBI)||299, 323|
|RSP_3022||RSP_3022||transcriptional regulator, TetR family (NCBI)||213, 323|
|RSP_3094||RSP_3094||Putative transmembrane anti-sigma factor (NCBI)||202, 323|
|RSP_3124||RSP_3124||transcriptional regulator, LysR family (NCBI)||1, 323|
|RSP_3125||RSP_3125||transcriptional regulator, ArsR familyy (NCBI)||1, 323|
|RSP_3229||RSP_3229||Membrane-bound lytic murein transglycosylase B (NCBI)||200, 262|
|RSP_3422||RSP_3422||hypothetical protein (NCBI)||251, 323|
|RSP_3592||aroA||EPSP synthase, 3-phosphoshikimate 1-carboxyvinyltransferase (NCBI)||203, 323|
|RSP_3597||RSP_3597||CorC/Hlyc family protein with CBS domains (NCBI)||182, 200|
|RSP_3598||RSP_3598||Protein of unknown function UPF0054 (NCBI)||182, 200|
|RSP_3599||RSP_3599||hypothetical protein (NCBI)||56, 200|
|RSP_3675||RSP_3675||Esterase/lipase/thioesterase (NCBI)||44, 323|
|RSP_3677||RSP_3677||ABC sugar transporter, ATPase subunit (NCBI)||44, 323|
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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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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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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