Organism : Bacillus subtilis | Module List :
molybdopterin synthase (small subunit) (RefSeq)
Functional Annotations (5)
|Molybdopterin converting factor, small subunit||cog/ cog|
|Mo-molybdopterin cofactor biosynthetic process||go/ biological_process|
|sulfur compound metabolic process||go/ biological_process|
|Sulfur relay system||kegg/ kegg pathway|
Regulation information for BSU14310(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 BSU14310
Module neighborhood information for BSU14310
|Gene||Common Name||Description||Module membership|
|BSU00080||yaaC||hypothetical protein (RefSeq)||105, 150|
|BSU00090||guaB||inosine 5'-monophosphate dehydrogenase (RefSeq)||42, 150|
|BSU00480||yabJ||putative enzyme resulting in alteration of gene expression (RefSeq)||128, 221|
|BSU00730||cysK||cysteine synthase (RefSeq)||80, 150|
|BSU03240||ycgQ||hypothetical protein (RefSeq)||150, 233|
|BSU05280||ydeO||putative integral inner membrane protein (RefSeq)||128, 378|
|BSU06010||ydiL||putative membrane protease (RefSeq)||39, 128|
|BSU06020||groES||co-chaperonin GroES (RefSeq)||39, 150|
|BSU06030||groEL||chaperonin GroEL (RefSeq)||39, 150|
|BSU06110||ydjA||BsuM intrinsic DNA restriction component (RefSeq)||128, 199|
|BSU06120||ydjB||hypothetical protein (RefSeq)||150, 409|
|BSU09080||yhcH||putative ABC transporter (ATP-binding protein) (RefSeq)||150, 233|
|BSU09110||yhcJ||putative ABC transporter (binding lipoprotein) (RefSeq)||128, 167|
|BSU11030||yitL||putative RNA-binding protein (RefSeq)||150, 247|
|BSU13250||ykoG||two-component response regulator [YkoH] (RefSeq)||146, 150|
|BSU13260||ykoH||two-component sensor histidine kinase [YkoG] (RefSeq)||146, 150|
|BSU13270||ykoI||hypothetical protein (RefSeq)||146, 150|
|BSU13480||ykrK||hypothetical protein (RefSeq)||150, 239|
|BSU14190||dapL||N-acetyl-diaminopimelate deacetylase (RefSeq)||128, 313|
|BSU14260||mobA||molybdopterin-guanine dinucleotide biosynthesis protein A (RefSeq)||128, 243|
|BSU14310||moaD||molybdopterin synthase (small subunit) (RefSeq)||128, 150|
|BSU14610||pdhD||dihydrolipoamide dehydrogenase (RefSeq)||128, 355|
|BSU14790||ylaI||hypothetical protein (RefSeq)||128, 324|
|BSU17680||thyA||thymidylate synthase (RefSeq)||128, 255|
|BSU17890||tkt||transketolase (RefSeq)||128, 273|
|BSU18300||ppsE||plipastatin synthetase (RefSeq)||98, 150|
|BSU18660||yoaM||hypothetical protein (RefSeq)||19, 150|
|BSU18800||penP||beta-lactamase precursor (RefSeq)||150, 274|
|BSU18840||xynA||endo-1,4-beta-xylanase (RefSeq)||128, 213|
|BSU22080||ypwA||metal-dependent carboxypeptidase (RefSeq)||128, 199|
|BSU22140||kduD||2-deoxy-D-gluconate 3-dehydrogenase (RefSeq)||150, 168|
|BSU22790||hbs||non-specific DNA-binding protein HBsu; signal recognition particle-like (SRP) component (RefSeq)||128, 197|
|BSU23070||serA||D-3-phosphoglycerate dehydrogenase (RefSeq)||15, 128|
|BSU23080||aroD||3-dehydroquinate dehydratase (RefSeq)||128, 231|
|BSU23360||ppiB||peptidyl-prolyl isomerase (RefSeq)||7, 128|
|BSU23510||xerD||site-specific tyrosine recombinase XerD (RefSeq)||7, 128|
|BSU25420||yqeW||putative Na+/anion cotransporter (RefSeq)||86, 150|
|BSU25550||rpsT||30S ribosomal protein S20 (RefSeq)||128, 197|
|BSU27250||yrhB||cystathionine beta-lyase (RefSeq)||80, 150|
|BSU27260||mccA||cystathionine beta-synthase for the reverse transsulfuration pathway (RefSeq)||80, 150|
|BSU27280||yrrT||putative AdoMet-dependent methyltransferase (RefSeq)||150, 195|
|BSU27570||yrzK||hypothetical protein (RefSeq)||150, 239|
|BSU29250||nrnA||oligoribonuclease (nanoRNAse), 3',5'-bisphosphate nucleotidase (RefSeq)||128, 324|
|BSU29400||ytlI||transcriptional regulator (LysR family) (RefSeq)||150, 333|
|BSU31440||patB||C-S lyase (RefSeq)||11, 128|
|BSU31460||kapB||factor required for KinB signal transduction and activation of the phosphorelay to sporulation (RefSeq)||145, 150|
|BSU32330||lipA||lipoyl synthase (RefSeq)||116, 128|
|BSU35220||minJ||topological determinant of cell division (RefSeq)||87, 128|
|BSU35250||ftsX||cell-division ABC transporter (RefSeq)||13, 128|
|BSU35640||lytA||membrane bound lipoprotein (RefSeq)||7, 128|
|BSU35850||ywtE||putative hydrolase (RefSeq)||128, 247|
|BSU36370||fabZ||(3R)-hydroxymyristoyl-ACP dehydratase (RefSeq)||128, 245|
|BSU36900||glyA||serine hydroxymethyltransferase (RefSeq)||128, 197|
|BSU38340||ywbF||putative sugar permease (RefSeq)||19, 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.
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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".
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.
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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
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