Organism : Desulfovibrio vulgaris Hildenborough | Module List :
Functional Annotations (5)
|Pyridoxal/pyridoxine/pyridoxamine kinase||cog/ cog|
|nucleic acid binding||go/ molecular_function|
|pyridoxal kinase activity||go/ molecular_function|
|Vitamin B6 metabolism||kegg/ kegg pathway|
|Metabolic pathways||kegg/ kegg pathway|
Regulation information for DVU0769(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 DVU0769
Module neighborhood information for DVU0769
|Gene||Common Name||Description||Module membership|
|DVU0135||hypothetical protein DVU0135||223, 278|
|DVU0450||ribF||riboflavin biosynthesis protein RibF||75, 278|
|DVU0478||serine/threonine protein phosphatase family protein||14, 150|
|DVU0489||paaK-1||phenylacetate-coenzyme A ligase||150, 176|
|DVU0571||ald||alanine dehydrogenase||150, 175|
|DVU0615||hypothetical protein DVU0615||150, 198|
|DVU0632||cupin family protein||150, 176|
|DVU0723||purT||phosphoribosylglycinamide formyltransferase 2||185, 278|
|DVU0724||sodium/alanine symporter family protein||223, 278|
|DVU0748||acs||acetyl-CoA synthetase||150, 296|
|DVU0767||class V aminotransferase||150, 337|
|DVU0768||murI||glutamate racemase||150, 278|
|DVU0769||pyridoxamine kinase||150, 278|
|DVU0808||gatA||aspartyl/glutamyl-tRNA amidotransferase subunit A||28, 278|
|DVU0869||uppS||undecaprenyl diphosphate synthase||28, 278|
|DVU1060||glycosyl transferase group 1 family protein||223, 278|
|DVU1215||PAP2 family protein||65, 278|
|DVU1252||hypothetical protein DVU1252||150, 250|
|DVU1454||ispD||2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase||5, 278|
|DVU1538||hypothetical protein DVU1538||28, 278|
|DVU1573||pth||peptidyl-tRNA hydrolase||82, 278|
|DVU1797||ksgA||dimethyladenosine transferase||75, 150|
|DVU1908||pdxJ||pyridoxine 5'-phosphate synthase||33, 150|
|DVU1944||pyruvate ferredoxin oxidoreductase, iron-sulfur binding subunit||150, 337|
|DVU2209||hypothetical protein DVU2209||176, 278|
|DVU2436||hypothetical protein DVU2436||223, 278|
|DVU2581||response regulator||141, 278|
|DVU2620||hypothetical protein DVU2620||150, 291|
|DVU2756||radical SAM domain-containing protein||62, 278|
|DVU2872||lambda family phage portal protein||106, 278|
|DVU2898||hypothetical protein DVU2898||81, 150|
|DVU2916||hemK||hemK protein||113, 278|
|DVU2945||hypothetical protein DVU2945||145, 278|
|DVU2995||glycosyl transferase group 1 family protein||150, 278|
|DVU2996||NAD-dependent epimerase/dehydratase family protein||87, 150|
|DVU2997||hypothetical protein DVU2997||87, 150|
|DVU2998||hypothetical protein DVU2998||87, 150|
|DVU3050||hypothetical protein DVU3050||174, 278|
|DVU3109||iron-sulfur cluster-binding protein||174, 278|
|DVU3116||prfC||peptide chain release factor 3||235, 278|
|DVU3207||RNB-like family protein||188, 278|
|DVU3223||aspB||aspartate aminotransferase||211, 278|
|DVU3287||glycosyl transferase group 2 family protein||46, 150|
|DVU3361||ADP-heptose synthase||211, 278|
|DVUA0061||hypothetical protein DVUA0061||53, 150|
|DVUA0112||type III secretion system protein YscC family||136, 150|
|DVUA0119||type III secretion system ATPase||136, 150|
|DVUA0124||sigma factor serine-protein kinase||136, 150|
|DVUA0132||CRISPR-associated Csh2 family protein||131, 150|
|DVUA0134||cas1||CRISPR-associated Cas1 family protein||150, 266|
|DVUA0135||CRISPR-associated Cas2 family protein||121, 150|
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