Organism : Clostridium acetobutylicum | Module List :
TRNA nucleotidyltransferase family enzyme (NCBI ptt file)
Functional Annotations (4)
|tRNA nucleotidyltransferase/poly(A) polymerase||cog/ cog|
|RNA binding||go/ molecular_function|
|polynucleotide adenylyltransferase activity||go/ molecular_function|
|RNA processing||go/ biological_process|
Regulation information for CAC2062(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 CAC2062
Module neighborhood information for CAC2062
|Gene||Common Name||Description||Module membership|
|CAC0414||CAC0414||Hypothetical protein (NCBI ptt file)||211, 249|
|CAC0478||CAC0478||ACT domain containing transcriptional regulators, related to gcvR of E.coli (NCBI ptt file)||211, 299|
|CAC1015||CAC1015||Pseudouridylate synthase (NCBI ptt file)||76, 306|
|CAC1234||pheB||Chorismate mutase PheB of B.subtilis ortholog (NCBI ptt file)||76, 215|
|CAC1251||rodA||Cell division protein, rodA/ftsW/spoVE family (NCBI ptt file)||76, 281|
|CAC1501||CAC1501||DNA-methyltransferase (cytosine-specific), ortholog of BSP6I Bsubtilis (NCBI ptt file)||76, 79|
|CAC1612||CAC1612||Probable cation efflux pump, multidrug resistance protein (FS) (NCBI ptt file)||76, 149|
|CAC1613||CAC1613||ABC-type multidrug/protein/lipid transport system, membrane ATPase component (NCBI ptt file)||76, 249|
|CAC1691||CAC1691||Predicted glycosyltransferase (NCBI ptt file)||201, 211|
|CAC1737||CAC1737||N6-adenine-specific methylase (NCBI ptt file)||211, 319|
|CAC1757||CAC1757||RimM protein, required for 16S rRNA processing (NCBI ptt file)||76, 297|
|CAC1758||trmD||TRNA-(guanine-N1)-methyltransferase, TrmD (NCBI ptt file)||76, 297|
|CAC1814||pgsA||Phosphatidylglycerophosphate synthase (NCBI ptt file)||211, 350|
|CAC1847||lytB/rpsA||Fusion Penicillin tolerance LytB domain (N-terminus) and S1 ribosomal protein (C-terminus) (NCBI ptt file)||211, 350|
|CAC1850||CAC1850||Transcriptional regulators, RpiR family (NCBI ptt file)||64, 211|
|CAC1851||CAC1851||Predicted pseudouridylate synthase (NCBI ptt file)||64, 211|
|CAC2060||CAC2060||Predicted transciptinal regulator (HTH-type), YPUH B.subtilis ortholog (NCBI ptt file)||211, 215|
|CAC2061||CAC2061||Uncharacterized ptotrin, YPUG B.subtilis ortholog (NCBI ptt file)||211, 215|
|CAC2062||CAC2062||TRNA nucleotidyltransferase family enzyme (NCBI ptt file)||76, 211|
|CAC2080||CAC2080||Predicted geranylgeranyl pyrophosphate synthase (NCBI ptt file)||211, 350|
|CAC2084||nusB||Transcription termination factor NusB (NCBI ptt file)||211, 350|
|CAC2228||CAC2228||Hypothetical protein (NCBI ptt file)||76, 281|
|CAC2315||CAC2315||DTDP-4-dehydrorhamnose reductase, rfbD ortholog (NCBI ptt file)||211, 350|
|CAC2316||CAC2316||Polysaccharide deacetylase-like protein; Xylanase/chitin deacetylase family enzyme (NCBI ptt file)||211, 350|
|CAC2317||tagA||Teichoic acid biosynthesis protein, tagA (NCBI ptt file)||84, 211|
|CAC2318||CAC2318||Membrane protein of EXOQ family, involved in exopolysaccharide production (NCBI ptt file)||211, 350|
|CAC2319||CAC2319||Hypothetical protein (NCBI ptt file)||211, 350|
|CAC2320||CAC2320||Predicted glycosyltransferase (NCBI ptt file)||211, 350|
|CAC2331||CAC2331||DTDP-4-dehydrorhamnose 3,5-epimerase (NCBI ptt file)||86, 211|
|CAC2339||CAC2339||Uncharacterized protein, YBBK B.subtilis ortholog (NCBI ptt file)||76, 123|
|CAC2373||CAC2373||Predicted membrane protein (NCBI ptt file)||76, 84|
|CAC2713||CAC2713||AT-rich DNA-binding protein (NCBI ptt file)||76, 281|
|CAC2852||comFC||Predicted amidophosphoribosyltransferase, ComFC B.suntilis ortholog (NCBI ptt file)||76, 149|
|CAC2855||CAC2855||Predicted membrane protein (NCBI ptt file)||59, 76|
|CAC2872||CAC2872||Predicted membrane protein in FoF1-type ATP synthase operon (NCBI ptt file)||76, 162|
|CAC2881||CAC2881||Protein-tyrosine-phosphatase, YWLE B.subtilis ortholog (NCBI ptt file)||35, 76|
|CAC2990||csp||Cold shock protein (NCBI ptt file)||32, 76|
|CAC3200||CAC3200||Predicted transcriptional regulator, homolog of Bvg accessory factor (NCBI ptt file)||76, 116|
|CAC3208||CAC3208||Uncharacterized protein, YABQ B.subtilis (NCBI ptt file)||211, 350|
|CAC3209||CAC3209||Uncharacterized protein, YABP B.subtilis (NCBI ptt file)||58, 211|
|CAC3537||CAC3537||Fragment of SECA (fragment) (NCBI ptt file)||76, 229|
|CAC3538||CAC3538||Metallo-beta-lactamase superfamily hydrolase (NCBI ptt file)||211, 350|
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.
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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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