Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
Regulation information for RSP_1201(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|
Module neighborhood information for RSP_1201
|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_0205||RSP_0205||hypothetical protein (NCBI)||213, 327|
|RSP_0220||RSP_0220||hypothetical protein (NCBI)||68, 327|
|RSP_0370||RSP_0370||hypothetical protein (NCBI)||210, 327|
|RSP_0381||RSP_0381||hypothetical protein (NCBI)||14, 43|
|RSP_0444||RSP_0444||hypothetical protein (NCBI)||43, 360|
|RSP_0591||RSP_0591||Cold-shock protein (NCBI)||56, 327|
|RSP_0626||infA||Probable translation initiation factor 1 (IF-1) (NCBI)||75, 327|
|RSP_0842||RSP_0842||putative porin (NCBI)||43, 310|
|RSP_0867||rnhA||ribonuclease H (NCBI)||213, 327|
|RSP_0887||MrcB||Glycosyl transferase, family 51 (NCBI)||43, 112|
|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_1059||rpmH||50S ribosomal protein L34 (NCBI)||75, 327|
|RSP_1064||RSP_1064||Putative preprotein translocase, YidC (NCBI)||43, 369|
|RSP_1104||RSP_1104||hypothetical protein (NCBI)||35, 327|
|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_1341||rpsT||Ribosomal protein S20 (NCBI)||75, 327|
|RSP_1388||RSP_1388||DNA-binding protein HU, form N (NCBI)||327, 345|
|RSP_1398||rpmJ||ribosomal protein L36 (NCBI)||75, 327|
|RSP_1496||RSP_1496||hypothetical protein (NCBI)||181, 327|
|RSP_1498||RSP_1498||hypothetical protein (NCBI)||181, 327|
|RSP_1517||spbA||Histone-like protein of HNS family (NCBI)||48, 327|
|RSP_1519||prrC||PrrC (NCBI)||43, 360|
|RSP_1529||trxA||Thioredoxin (NCBI)||327, 345|
|RSP_1667||RSP_1667||hypothetical protein (NCBI)||43, 112|
|RSP_1668||FolK||2-amino-4-hydroxy-6- hydroxymethyldihydropteridine pyrophosphokinase (NCBI)||43, 112|
|RSP_1669||rpoZ||RNA polymerase omega subunit (NCBI)||75, 327|
|RSP_1860||RSP_1860||hypothetical protein (NCBI)||43, 377|
|RSP_1887||RSP_1887||Ribosomal protein L33 (NCBI)||75, 327|
|RSP_2016||rpmB||50S ribosomal protein L28 (NCBI)||248, 327|
|RSP_2258||purC||SAICAR synthetase (NCBI)||43, 109|
|RSP_2424||RSP_2424||ferredoxin II (NCBI)||75, 327|
|RSP_2425||RSP_2425||putative CarD-like transcriptional regulator (NCBI)||43, 112|
|RSP_2463||acpP||Acyl carrier protein (ACP) (NCBI)||327, 345|
|RSP_2536||rhlE||ATP-dependent helicase, DEAD-box (NCBI)||43, 195|
|RSP_2630||gyrA||DNA gyrase/topoisomerase IV, subunit A (NCBI)||43, 182|
|RSP_2711||RSP_2711||putative outer membrane protein (NCBI)||43, 360|
|RSP_2974||RSP_2974||Putative metalopeptidase (NCBI)||43, 118|
|RSP_3595||metK||S-adenosylmethionine synthetase (NCBI)||43, 85|
|RSP_4294||RSP_4294||16S ribosomal RNA (NCBI)||14, 43|
|RSP_4300||RSP_4300||tRNA-Ser (NCBI)||327, 336|
|RSP_4301||RSP_4301||tRNA-Leu (NCBI)||48, 327|
|RSP_4309||RSP_4309||tRNA-Val (NCBI)||75, 327|
|RSP_4311||RSP_4311||tRNA-Pro (NCBI)||75, 327|
|RSP_4323||RSP_4323||tRNA-OTHER (NCBI)||75, 327|
|RSP_4332||RSP_4332||tRNA-Leu (NCBI)||75, 327|
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.
You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".
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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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