Organism : Clostridium acetobutylicum | Module List :
Small basic protein, sbp, uncharacterized (NCBI ptt file)
Functional Annotations (1)
|Uncharacterized conserved protein (small basic protein)||cog/ cog|
Regulation information for CAC2123(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 CAC2123
|Uncharacterized conserved protein (small basic protein)||cog/ cog|
Module neighborhood information for CAC2123
|Gene||Common Name||Description||Module membership|
|CAC0029||CAC0029||Distantly related to cell wall-associated hydrolases, similar to yycO Bacillus subtilis (NCBI ptt file)||67, 99|
|CAC0030||CAC0030||Hypothetical protein (NCBI ptt file)||67, 99|
|CAC0091||ilvC||Ketol-acid reductoisomerase (NCBI ptt file)||128, 334|
|CAC0140||CAC0140||Predicted permease (NCBI ptt file)||67, 114|
|CAC0270||CAC0270||Hypothetical protein (NCBI ptt file)||67, 225|
|CAC0288||CAC0288||ABC transporter, ATP-binding protein (NCBI ptt file)||67, 266|
|CAC0711||tpi||Triosephosphate isomerase (NCBI ptt file)||128, 292|
|CAC0713||eno||Enolase (NCBI ptt file)||128, 363|
|CAC0830||CAC0830||Response regulator (NCBI ptt file)||67, 115|
|CAC0843||CAC0843||Ribonuclease precursor (barnase), secreted. (NCBI ptt file)||65, 67|
|CAC0844||CAC0844||Barstar-like protein ribonuclease (barnase) inhibitor (NCBI ptt file)||67, 341|
|CAC1264||lytR||Membrane bound transcriptional regulator of LytR family (NCBI ptt file)||67, 248|
|CAC1266||CAC1266||Pseudouridylate synthase family protein, yabo B.subtilis ortholog (NCBI ptt file)||67, 345|
|CAC1280||hrcA||Transcriptional regulator of heat shock genes, HrcA (NCBI ptt file)||128, 201|
|CAC1281||grpE||Molecular chaperone GrpE (NCBI ptt file)||128, 221|
|CAC1283||dnaJ||Molecular chaperones DnaJ (HSP40 family) (NCBI ptt file)||128, 221|
|CAC1287||CAC1287||HIT family hydrolase (NCBI ptt file)||128, 289|
|CAC1288||rpsU||Ribosomal protein S21 (NCBI ptt file)||128, 231|
|CAC1679||CAC1679||Hypothetical protein (NCBI ptt file)||64, 128|
|CAC1682||CAC1682||Ferric uptake regulation protein (NCBI ptt file)||128, 289|
|CAC1816||CAC1816||HD superfamily hydrolase, YMDA B.subtilis ortholog (NCBI ptt file)||128, 233|
|CAC1958||CAC1958||Predicted aldo/keto reductase, YTBE/YVGN B.subtilis ortholog (NCBI ptt file)||128, 289|
|CAC2040||CAC2040||ABC transported MDR-type, ATPase component (NCBI ptt file)||67, 248|
|CAC2071||CAC2071||Spo0A protein, (CheY-like receiver domain and HTH-type DNA binding domain) (NCBI ptt file)||128, 289|
|CAC2119||CAC2119||Predicted integral membrane protein, YggT family (NCBI ptt file)||128, 295|
|CAC2122||CAC2122||Conserved membrane protein (NCBI ptt file)||67, 231|
|CAC2123||sbp||Small basic protein, sbp, uncharacterized (NCBI ptt file)||67, 128|
|CAC2124||CAC2124||Conserved membrane protein (NCBI ptt file)||67, 128|
|CAC2334||CAC2334||UDP-glucose 4-epimerase (NCBI ptt file)||128, 289|
|CAC2335||CAC2335||UTP-glucose-1-phosphate uridylyltransferase (NCBI ptt file)||128, 289|
|CAC2556||CAC2556||Endoglucanase, family 26; S-layer homology domain (NCBI ptt file)||67, 184|
|CAC2571||CAC2571||Predicted acetyltransferase (NCBI ptt file)||67, 294|
|CAC2572||CAC2572||Possible aminoglycoside phosphotransferase (protein kinase related), diverged (NCBI ptt file)||67, 329|
|CAC2639||clpX||ATP-dependent protease Clp, ATPase subunit ClpX (NCBI ptt file)||128, 233|
|CAC2640||clpP||Protease subunits of ATP-dependent protease, ClpP (NCBI ptt file)||128, 289|
|CAC2688||CAC2688||Alpha/beta superfamily hydrolase (possible chloroperoxidase) (NCBI ptt file)||67, 238|
|CAC2752||CAC2752||Uncharacterized membrane protein, YPAA B.subtilis ortholog (NCBI ptt file)||67, 218|
|CAC2786||CAC2786||Uncharacterized conserved protein, YQGV B.subtilis ortholog (NCBI ptt file)||67, 277|
|CAC2787||CAC2787||Serine/threonine protein phosphatase (NCBI ptt file)||109, 128|
|CAC2808||CAC2808||Beta-lactamase class C domain (PBPX family) containing protein (NCBI ptt file)||67, 248|
|CAC2847||CAC2847||Ribosome-associated protein Y (PSrp-1) (NCBI ptt file)||128, 201|
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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