Organism : Desulfovibrio vulgaris Hildenborough | Module List :
Regulation information for DVU3136(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
|Motif Id||e-value||Consensus||Motif Logo||RegPredict|
Functional Enrichment for DVU3136
Module neighborhood information for DVU3136
|Gene||Common Name||Description||Module membership|
|DVU0111||response regulator||143, 274|
|DVU0239||hypothetical protein DVU0239||153, 274|
|DVU0298||hypothetical protein DVU0298||110, 120|
|DVU0453||ATP-dependent DNA helicase UvrD||71, 274|
|DVU0577||formate dehydrogenase formation protein FdhE||274, 281|
|DVU0579||molybdopterin-guanine dinucleotide biosynthesis protein A||274, 281|
|DVU0587||fdnG-1||formate dehydrogenase subunit alpha, selenocysteine-containing||167, 274|
|DVU0727||hypothetical protein DVU0727||90, 110|
|DVU0728||hypothetical protein DVU0728||90, 110|
|DVU0756||hypothetical protein||90, 110|
|DVU0801||uvrC||excinuclease ABC subunit C||57, 110|
|DVU0819||FMN reductase, NADPH-dependent||153, 274|
|DVU0866||dxr||1-deoxy-D-xylulose 5-phosphate reductoisomerase||110, 226|
|DVU0955||alr||alanine racemase||110, 225|
|DVU0985||hypothetical protein DVU0985||57, 110|
|DVU1013||TolC family type I secretion outer membrane protein||4, 110|
|DVU1151||hypothetical protein DVU1151||90, 110|
|DVU1396||hypothetical protein DVU1396||192, 274|
|DVU1412||glycerate dehydrogenase||236, 274|
|DVU1554||radical SAM domain-containing protein||110, 242|
|DVU1564||hypothetical protein DVU1564||263, 274|
|DVU1592||arginine N-succinyltransferase subunit beta||192, 274|
|DVU1593||cheY-1||chemotaxis protein CheY||123, 274|
|DVU1594||cheA-1||chemotaxis protein CheA||192, 274|
|DVU1595||cheR-1||chemotaxis protein methyltransferase||274, 277|
|DVU1596||cheB-1||protein-glutamate methylesterase CheB||192, 274|
|DVU1597||sulfite reductase, assimilatory-type||123, 274|
|DVU1628||rpoN||RNA polymerase sigma-54 factor||90, 110|
|DVU1645||ArsR family transcriptional regulator||110, 226|
|DVU1973||rhodanese-like domain-containing protein||269, 274|
|DVU1974||pyridine nucleotide-disulfide oxidoreductase||274, 283|
|DVU2282||hypothetical protein DVU2282||110, 173|
|DVU2309||methyl-accepting chemotaxis protein||90, 110|
|DVU2362||thiE||thiamine-phosphate pyrophosphorylase||66, 110|
|DVU2421||4-oxalocrotonate tautomerase family protein||192, 274|
|DVU2422||nitroreductase family protein||192, 274|
|DVU2439||RND family efflux transporter MFP subunit||4, 110|
|DVU2548||acpD||ACP phosphodiesterase||110, 194|
|DVU2662||hypothetical protein DVU2662||110, 226|
|DVU2972||chemotaxis protein CheD||37, 274|
|DVU3041||cytochrome c553||178, 274|
|DVU3076||hypothetical protein DVU3076||269, 274|
|DVU3079||glyoxalase family protein||110, 274|
|DVU3135||flavodoxin-like fold domain-containing protein||110, 274|
|DVU3136||nitroreductase family protein||110, 274|
|DVU3316||pyrD||dihydroorotate dehydrogenase||4, 110|
|DVUA0023||ABC transporter permease||192, 274|
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.
Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.
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".
For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.
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.
This help page. More general help can be accessed by clicking help menu in the main navigation bar.
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
- 6. Visualisation legend