Organism : Clostridium acetobutylicum | Module List :
Regulation information for CAC3531(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 CAC3531
Module neighborhood information for CAC3531
|Gene||Common Name||Description||Module membership|
|CAC0122||cheY||Chemotaxis respons regulator (cheY) (NCBI ptt file)||167, 247|
|CAC0132||CAC0132||Hypothetical protein (NCBI ptt file)||247, 270|
|CAC0134||CAC0134||Hypothetical protein, CF-19 family (NCBI ptt file)||62, 247|
|CAC0135||CAC0135||Hypothetical protein, CF-23 family (NCBI ptt file)||13, 247|
|CAC0295||CAC0295||Metal-dependent amidohydrolases (NCBI ptt file)||108, 190|
|CAC0343||CAC0343||Hypothetical protein, CF-23 family (NCBI ptt file)||190, 258|
|CAC0419||CAC0419||Predicted membrane protein (NCBI ptt file)||247, 351|
|CAC0420||CAC0420||Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file)||185, 247|
|CAC0477||CAC0477||AP superfamily (NCBI ptt file)||247, 258|
|CAC0487||CAC0487||Uncharacterized protein, ortholog of Thermotoga maritima (4981823) (NCBI ptt file)||247, 259|
|CAC0619||CAC0619||Nitrate ABC transporter ATP binding protein (NCBI ptt file)||190, 270|
|CAC0626||trpS||Tryptophan-tRNA synthetase, trpS (NCBI ptt file)||247, 296|
|CAC0670||CAC0670||Hypothetical protein (NCBI ptt file)||169, 190|
|CAC0671||CAC0671||Ortholog yrbG, yetE, ykjA, ydfS, ydfR B.subtilis (NCBI ptt file)||169, 190|
|CAC0924||CAC0924||Predicted membrane protein (NCBI ptt file)||145, 190|
|CAC0955||CAC0955||ATP-dependent Zn protease (NCBI ptt file)||150, 190|
|CAC1271||CAC1271||ComC competence related protein (NCBI ptt file)||190, 312|
|CAC1350||CAC1350||Hypothetical protein (NCBI ptt file)||102, 190|
|CAC1359||CAC1359||Predicted xylanase/chitin deacetylase (NCBI ptt file)||150, 190|
|CAC1495||CAC1495||Enzyme of dihydrofolate reductase family, ortholog YWFD B.subtilis (NCBI ptt file)||5, 247|
|CAC1525||CAC1525||Uncharacterized protein, homolog of PHNB E.coli (NCBI ptt file)||169, 190|
|CAC1865||CAC1865||Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file)||190, 336|
|CAC1959||CAC1959||Uncharacterized protein, YYAC B.subtilis homolog (fragment) (NCBI ptt file)||190, 208|
|CAC2039||CAC2039||Hypothetical protein, CF-5 family (NCBI ptt file)||44, 190|
|CAC2242||CAC2242||Predicted transcriptional regulator, arsE family (NCBI ptt file)||214, 247|
|CAC2454||CAC2454||Hypothetical protein, CF-13 family (NCBI ptt file)||190, 264|
|CAC2506||CAC2506||SpoIID-like domain containing protein; peptidoglycan-binding domain (NCBI ptt file)||102, 190|
|CAC2560||CAC2560||Predicted acetyltransferase (NCBI ptt file)||69, 190|
|CAC2567||CAC2567||Superoxide dismutase (Fe/Mn family) (NCBI ptt file)||141, 190|
|CAC2614||CAC2614||Beta-phosphoglucomutase (NCBI ptt file)||141, 190|
|CAC2824||CAC2824||N-terminal HKD family nuclease fused to DNA/RNA helicases of superfamily II,conserved in Streptomyces (NCBI ptt file)||154, 247|
|CAC2902||CAC2902||Isopentenyl monophosphate kinase, IPK (NCBI ptt file)||66, 247|
|CAC2908||CAC2908||Spore coat protein cotS related (NCBI ptt file)||190, 312|
|CAC2909||CAC2909||Spore coat protein cotS related (diverged) (NCBI ptt file)||114, 190|
|CAC2910||CAC2910||Spore coat protein cotS related (NCBI ptt file)||190, 312|
|CAC2973||kdgA||2-keto-3-deoxy-6-phosphogluconate aldolase, eda/kdgA (NCBI ptt file)||108, 247|
|CAC3232||CAC3232||Hypothetical protein (NCBI ptt file)||62, 247|
|CAC3236||CAC3236||Possible transcriptional regulator from YAEG/LRPR family (NCBI ptt file)||247, 312|
|CAC3246||CAC3246||Hypothetical protein (NCBI ptt file)||145, 190|
|CAC3307||CAC3307||TPR-repeats containing protein (NCBI ptt file)||109, 190|
|CAC3308||CAC3308||Glycosyltransferase fused to TPR-repeat domain (NCBI ptt file)||3, 190|
|CAC3310||CAC3310||Predicted UDP-glucose 6-dehydrogenase (NCBI ptt file)||19, 190|
|CAC3380||CAC3380||Metallo-beta-lactamase superfamily hydrolase (NCBI ptt file)||108, 247|
|CAC3416||CAC3416||Uncharacterized protein, homolog of YYBI B.subtilis fused to uncharacterized domain similar to A.thaliana (gi:3292817 and 5002526) (NCBI ptt file)||190, 361|
|CAC3480||CAC3480||Hypothetical protein (NCBI ptt file)||141, 190|
|CAC3481||CAC3481||Transcriptional regulator, AcrR family (NCBI ptt file)||167, 247|
|CAC3524||CAC3524||Hypothetical protein, CF-7 family (NCBI ptt file)||226, 247|
|CAC3531||CAC3531||IS605/IS200-like transposase (NCBI ptt file)||190, 247|
|CAC3549||CAC3549||Subtilisin-like serine protease (NCBI ptt file)||150, 190|
|CAC3562||CAC3562||HD superfamily hydrolase (NCBI ptt file)||127, 247|
|CAC3563||CAC3563||Mismatch repair protein MutS-like ATPase (NCBI ptt file)||247, 335|
|CAC3649||spoVT||Possible stage V sporulation protein T, transcriptional regulator AbrB homolog (NCBI ptt file)||108, 247|
|CAC3677||kdpE||KDP operon transcriptional regulatory protein KdpE (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)||108, 247|
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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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)
- 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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