Organism : Clostridium acetobutylicum | Module List :
Nifs family aminotransferase (NCBI ptt file)
Functional Annotations (6)
|Selenocysteine lyase||cog/ cog|
|metabolic process||go/ biological_process|
|transaminase activity||go/ molecular_function|
|selenocysteine lyase activity||go/ molecular_function|
|pyridoxal phosphate binding||go/ molecular_function|
Regulation information for CAC2354(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 CAC2354
Module neighborhood information for CAC2354
|Gene||Common Name||Description||Module membership|
|CAC0011||CAC0011||Uncharacterized conserved of ErfK family (NCBI ptt file)||113, 279|
|CAC0205||CAC0205||Predicted phosphohydrolases, Icc family (NCBI ptt file)||62, 279|
|CAC0262||CAC0262||Tryptophan-rich possible sensory protein, TSPO homolog (NCBI ptt file)||95, 279|
|CAC0354||CAC0354||Uncharacterized membrane protein (NCBI ptt file)||279, 312|
|CAC0473||dnaK||DnaK protein (heat shock protein), C-terminal region has VWA type A domain (NCBI ptt file)||14, 41|
|CAC0512||CAC0512||Uncharacterized conserved protein, YbhK/UPF0052 family (NCBI ptt file)||41, 343|
|CAC0513||CAC0513||Uncharacterized conserved protein, similar to B.subtilis yvcL (NCBI ptt file)||41, 154|
|CAC0531||CAC0531||Transcriptional regulator, RpiR family (NCBI ptt file)||41, 64|
|CAC0604||CAC0604||Acyl carrier protein phosphodiesterase (NCBI ptt file)||57, 279|
|CAC0793||CAC0793||Uncharacterized conserved protein of probably eukaryotic origin (NCBI ptt file)||279, 314|
|CAC0959||clpB||ATPase with chaperone activity, two ATP-binding domains (NCBI ptt file)||6, 41|
|CAC1474||CAC1474||Proline/glycine betaine ABC transport system, periplasmic component (NCBI ptt file)||41, 177|
|CAC1475||CAC1475||Proline/glycine betaine ABC transport system, ATPase component (NCBI ptt file)||41, 177|
|CAC1520||CAC1520||Hypothetical protein (NCBI ptt file)||118, 279|
|CAC1553||CAC1553||Membrane associated sensory transduction histidine kinase (with HAMP domain) (NCBI ptt file)||41, 265|
|CAC1657||CAC1657||Uncharacterized conserved protein, yisX B.subtilis ortholog (NCBI ptt file)||279, 326|
|CAC1662||CAC1662||Hypothetical protein (NCBI ptt file)||142, 279|
|CAC1665||CAC1665||Predicted amidohydrolase (NCBI ptt file)||41, 113|
|CAC1964||rpsA||Ribosomal protein S1 (NCBI ptt file)||41, 47|
|CAC1985||CAC1985||Hypothetical protein (NCBI ptt file)||279, 300|
|CAC2034||CAC2034||Hypothetical protein (NCBI ptt file)||38, 279|
|CAC2052||CAC2052||DNA-dependent RNA polymerase sigma subunit (NCBI ptt file)||41, 64|
|CAC2053||CAC2053||Hypothetical protein (NCBI ptt file)||41, 64|
|CAC2089||CAC2089||Stage III sporulation protein AE, SpoIIIAE (NCBI ptt file)||263, 279|
|CAC2143||sigD||Sigma factor of SigD/WhiG family (NCBI ptt file)||14, 41|
|CAC2144||CAC2144||Uncharacterized protein, YPFA B.subtilis ortholog (NCBI ptt file)||14, 41|
|CAC2145||CAC2145||ATPases involved in chromosome partitioning, MinD family, YLXH B.subtilis ortholog (NCBI ptt file)||14, 41|
|CAC2345||CAC2345||Glycosyltransferase (NCBI ptt file)||100, 279|
|CAC2352||CAC2352||Hypothetical protein (NCBI ptt file)||279, 330|
|CAC2353||CAC2353||Hypothetical protein (NCBI ptt file)||279, 330|
|CAC2354||CAC2354||Nifs family aminotransferase (NCBI ptt file)||41, 279|
|CAC2363||CAC2363||Uncharacterized protein, YtxC B.subtilis homolog (NCBI ptt file)||95, 279|
|CAC2412||CAC2412||Hypothetical protein (NCBI ptt file)||105, 279|
|CAC2458||CAC2458||2-oxoacid ferredoxin oxidoreductase, beta subunit (NCBI ptt file)||41, 200|
|CAC2459||CAC2459||2-oxoacid:ferredoxin oxidoreductase, alpha subunit (NCBI ptt file)||142, 279|
|CAC2542||CAC2542||FAD/FMN-containing dehydrogenase (NCBI ptt file)||41, 265|
|CAC2543||etfA||Electron-transferring flavoprotein large subunit (NCBI ptt file)||41, 363|
|CAC2544||etfB||Electron-transferring flavoprotein small subunit (NCBI ptt file)||41, 291|
|CAC2569||CAC2569||NimC/NimA family protein (NCBI ptt file)||279, 320|
|CAC2625||CAC2625||Predicted membrane protein (NCBI ptt file)||41, 113|
|CAC2638||lonB||Lon-like ATP-dependent protease (NCBI ptt file)||41, 177|
|CAC2679||CAC2679||Pullulanase (NCBI ptt file)||267, 279|
|CAC2843||CAC2843||Protein containing aminopeptidase domain (iap family) (NCBI ptt file)||39, 279|
|CAC2863||CAC2863||Predicted membrane protein (NCBI ptt file)||102, 279|
|CAC2941||CAC2941||HAD superfamily hydrolase (NCBI ptt file)||47, 279|
|CAC2945||CAC2945||Possible phosphoglycerate dehydrogenase (NCBI ptt file)||279, 363|
|CAC3030||CAC3030||Hypothetical protein (NCBI ptt file)||41, 265|
|CAC3031||hisC||Histidinol-phosphate aminotransferase (NCBI ptt file)||142, 279|
|CAC3080||CAC3080||Hypothetical protein (NCBI ptt file)||39, 41|
|CAC3204||CAC3204||Cell cycle protein MesJ ortholog, ATPase of the PP-loop superamily (NCBI ptt file)||142, 279|
|CAC3658||CAC3658||Uncharacterized conserved membrane protein, SapB/MtgC family (NCBI ptt file)||41, 272|
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.
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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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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
- 5. Module(s) that source gene and target genes belong to
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