Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Probable transposase (NCBI)
Functional Annotations (5)
|Transposase and inactivated derivatives||cog/ cog|
|DNA binding||go/ molecular_function|
|transposase activity||go/ molecular_function|
|transposition, DNA-mediated||go/ biological_process|
|sequence-specific DNA binding||go/ molecular_function|
Regulation information for RSP_3012(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_3012
Module neighborhood information for RSP_3012
|Gene||Common Name||Description||Module membership|
|RSP_0118||RSP_0118||Cytochrome c oxidase, subunit IIc (NCBI)||77, 229|
|RSP_0327||nnrR||Crp-Fnr regulatory protein (NnrR) (NCBI)||4, 126|
|RSP_0406||RSP_0406||periplasmic sensor diguanylate cyclase (GGDEF) (NCBI)||126, 175|
|RSP_0607||RSP_0607||sigma 24 (NCBI)||77, 103|
|RSP_0876||RSP_0876||Chromosome segregation protein SMC2 (NCBI)||126, 302|
|RSP_0878||RSP_0878||putative acetyltransferase protein (NCBI)||126, 294|
|RSP_0987||RSP_0987||Putative transporter, RarD family, DMT superfamily (NCBI)||84, 126|
|RSP_1040||RSP_1040||transcriptional regulator, ArsR family (NCBI)||98, 126|
|RSP_1361||RSP_1361||hypothetical protein (NCBI)||126, 174|
|RSP_1369||RSP_1369||Short-chain dehydrogenase/reductase SDR (NCBI)||126, 215|
|RSP_1371||RSP_1371||putative 2-dehydro-3-deoxygalactonokinase (NCBI)||126, 136|
|RSP_1602||RSP_1602||TRAP-T family transporter, DctM (12TMs) subunit (NCBI)||32, 77|
|RSP_1604||RSP_1604||TRAP-T family transporter, DctQ (4TMs) subunit (NCBI)||32, 77|
|RSP_1605||RSP_1605||TRAP-T family transporter, periplasmic binding protein, DctP (NCBI)||32, 77|
|RSP_1607||RSP_1607||Putative regulatory protein, GntR family (NCBI)||77, 214|
|RSP_1636||RSP_1636||phage-related protein, probable phage tail tape meausure protein, lambda family (NCBI)||31, 77|
|RSP_1663||RSP_1663||putative transcriptional regulator, LacI family (NCBI)||81, 126|
|RSP_1830||surf-1||Surf1 protein (NCBI)||126, 356|
|RSP_1835||RSP_1835||Putative FAD dependent oxidoreductase (NCBI)||126, 322|
|RSP_1896||RSP_1896||probable guanine deaminase (NCBI)||63, 126|
|RSP_1927||RSP_1927||hypothetical protein (NCBI)||126, 331|
|RSP_2017||RSP_2017||hypothetical protein (NCBI)||23, 126|
|RSP_2070||RSP_2070||Putative Phage-related terminase (NCBI)||77, 304|
|RSP_2071||RSP_2071||hypothetical protein (NCBI)||77, 304|
|RSP_2165||putR||transcriptional regulator, AsnC family (NCBI)||107, 126|
|RSP_2168||RSP_2168||hypothetical protein (NCBI)||126, 175|
|RSP_2182||betI||transcriptional regulator, BetI (NCBI)||77, 303|
|RSP_2183||betB||Betaine aldehyde dehydrogenase (NCBI)||77, 303|
|RSP_2184||betA||Choline dehydrogenase (NCBI)||77, 303|
|RSP_2390||acuC1||putative Acetoin utilization protein (NCBI)||126, 340|
|RSP_2391||RSP_2391||2'-5' RNA ligase (NCBI)||126, 215|
|RSP_2555||RSP_2555||hypothetical protein (NCBI)||77, 157|
|RSP_2556||RSP_2556||hypothetical protein (NCBI)||77, 157|
|RSP_2750||RSP_2750||hypothetical protein (NCBI)||77, 105|
|RSP_2753||RSP_2753||hypothetical protein (NCBI)||77, 105|
|RSP_2755||RSP_2755||hypothetical protein (NCBI)||74, 77|
|RSP_2792||RSP_2792||putative monooxygenase alpha subunit (NCBI)||77, 103|
|RSP_2796||RSP_2796||hypothetical protein (NCBI)||77, 103|
|RSP_2798||groEL3||Putative chaperonin groEL (NCBI)||77, 103|
|RSP_2914||RSP_2914||Nucleoside hydrolase (NCBI)||126, 309|
|RSP_2944||RSP_2944||hypothetical protein (NCBI)||77, 153|
|RSP_2995||RSP_2995||possible phage major capsid protein, gp36 (NCBI)||77, 153|
|RSP_3012||RSP_3012||Probable transposase (NCBI)||77, 126|
|RSP_3065||RSP_3065||Putative transporter, Major facilitator superfamily (MFS) (NCBI)||77, 320|
|RSP_3114||RSP_3114||hypothetical protein (NCBI)||77, 282|
|RSP_3259||RSP_3259||Transcription antitermination protein (NCBI)||77, 236|
|RSP_3380||RSP_3380||hypothetical protein (NCBI)||77, 236|
|RSP_3393||RSP_3393||ABC opine/polyamine transporter, inner membrane subunit (NCBI)||77, 88|
|RSP_3420||RSP_3420||Methyl-accepting chemotaxis protein (NCBI)||77, 251|
|RSP_3421||RSP_3421||hypothetical protein (NCBI)||77, 105|
|RSP_3605||RSP_3605||FAD-dependent pyridine nucleotide-disulphide oxidoreductase (NCBI)||77, 273|
|RSP_3788||RSP_3788||hypothetical protein (NCBI)||77, 233|
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
- 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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