Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Putative transporter, DMT superfamily (NCBI)
Functional Annotations (1)
Regulation information for RSP_1390(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_1390
Module neighborhood information for RSP_1390
|Gene||Common Name||Description||Module membership|
|RSP_0366||RSP_0366||Adenylosuccinate synthetase (NCBI)||192, 258|
|RSP_0633||RSP_0633||UDP-N-acetylglucosamine enolpyruvyl transferase (NCBI)||192, 349|
|RSP_0687||RSP_0687||Predicted hydrolase (haloacid dehalogenase (HAD) superfamily) (NCBI)||192, 209|
|RSP_0725||RSP_0725||Thioredoxin, thioldisulfide interchange protein (NCBI)||51, 192|
|RSP_0744||RSP_0744||DNA-3-methyladenine glycosylase I (NCBI)||192, 349|
|RSP_0764||RSP_0764||Multi Antimicrobial Extrusion (MATE) family efflux pump NorM (NCBI)||192, 349|
|RSP_0832||RSP_0832||Putative GTP-binding protein (NCBI)||166, 192|
|RSP_0916||pmbA||Putative PmbA/TldD protein invoved in modulation of DNA gyrase (NCBI)||192, 218|
|RSP_0934||gpmI||Phosphoglycerate mutase, 2,3-bisphosphoglycerate-independent (NCBI)||192, 299|
|RSP_1068||argB||acetylglutamate kinase (NCBI)||109, 192|
|RSP_1131||dapD||2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (NCBI)||25, 192|
|RSP_1150||bacA||Bacitracin Resistance Protein (NCBI)||192, 349|
|RSP_1151||RSP_1151||NADH-ubiquinone oxidoreductase (NCBI)||192, 349|
|RSP_1152||rnd||Ribonuclease D (NCBI)||192, 356|
|RSP_1153||GutQ||Sugar phosphate Isomerase (NCBI)||109, 192|
|RSP_1221||rph||ribonuclease PH (NCBI)||192, 258|
|RSP_1222||ham1||putative Ham1p_like protein, Ham1 family (NCBI)||192, 258|
|RSP_1339||RSP_1339||Formamidopyrimidine-DNA glycolase (NCBI)||84, 331|
|RSP_1346||RSP_1346||DNA gyrase, subunit B (NCBI)||192, 372|
|RSP_1372||RSP_1372||Major facilitator superfamily (MFS) transporter (NCBI)||289, 331|
|RSP_1376||asd||putative aspartate-semialdehyde dehydrogenase (NCBI)||166, 192|
|RSP_1390||RSP_1390||Putative transporter, DMT superfamily (NCBI)||192, 331|
|RSP_1580||lgt||Prolipoprotein diacylglyceryl transferase (NCBI)||192, 339|
|RSP_1795||serS||Probable Seryl-tRNA synthetase (NCBI)||109, 192|
|RSP_1831||thrC||Threonine synthase (NCBI)||109, 192|
|RSP_1892||RSP_1892||putative Cro/CI transcriptional regulator (NCBI)||313, 331|
|RSP_1927||RSP_1927||hypothetical protein (NCBI)||126, 331|
|RSP_2009||argF||Aspartate/ornithine carbamoyltransferase (NCBI)||192, 372|
|RSP_2358||RSP_2358||possible phage phi-C31 gp36-like protein / Major capsid protein, HK97 family (NCBI)||221, 331|
|RSP_2359||RSP_2359||hypothetical protein (NCBI)||161, 331|
|RSP_2360||RSP_2360||putative head portal protein, HK97 family (NCBI)||161, 331|
|RSP_2647||RSP_2647||Predicted SAM-dependent methyltransferases (NCBI)||192, 372|
|RSP_2929||RSP_2929||putative disulfide bond formation protein DsbB (NCBI)||2, 331|
|RSP_2968||RSP_2968||Probable dihydrolipoamide dehydrogenase (NCBI)||184, 192|
|RSP_3054||RSP_3054||hypothetical protein (NCBI)||247, 331|
|RSP_3073||RSP_3073||ErfK/YbiS/YcfS/YnhG family protein (NCBI)||188, 331|
|RSP_3117||RSP_3117||hypothetical protein (NCBI)||161, 331|
|RSP_3242||RSP_3242||Putative trypsin-like serine protease (NCBI)||253, 331|
|RSP_3329||RSP_3329||hypothetical protein (NCBI)||133, 331|
|RSP_3386||RSP_3386||TRAP-T family transporter, periplasmic binding protein (NCBI)||220, 331|
|RSP_3416||RSP_3416||ABC Fe+3-siderophore transporter, periplasmic binding protein (NCBI)||74, 331|
|RSP_3514||RSP_3514||transcriptional regulator, AraC family (NCBI)||288, 331|
|RSP_3515||RSP_3515||ABC polyamine/opine transporter, periplasmic binding protein (NCBI)||288, 331|
|RSP_3517||RSP_3517||ABC polyamine/opine transporter, inner membrane subunit (NCBI)||331, 379|
|RSP_3519||RSP_3519||putative proline racemase (NCBI)||282, 331|
|RSP_3567||znuB||ABC zinc tranporter, inner membrane subunit ZnuB (NCBI)||161, 331|
|RSP_3568||znuC||ABC zinc transporter, ATPase subunit ZnuC (NCBI)||161, 331|
|RSP_3569||zur||Zinc-uptake regulator, Zur (NCBI)||161, 331|
|RSP_3571||znuA||ABC zinc transporter, periplasmic binding protein ZnuA (NCBI)||161, 331|
|RSP_3664||RSP_3664||transcriptional regulator, GntR family (NCBI)||268, 331|
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.
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
- 3. Target genes (other module members)
- 4. Interactions between source and target genes for a particular module
- 5. Module(s) that source gene and target genes belong to
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