Organism : Clostridium acetobutylicum | Module List :
Uncharacterized, alkaline shock induced protein (NCBI ptt file)
Functional Annotations (1)
|Uncharacterized protein conserved in bacteria||cog/ cog|
Regulation information for CAC1734(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 CAC1734
|Uncharacterized protein conserved in bacteria||cog/ cog|
Module neighborhood information for CAC1734
|Gene||Common Name||Description||Module membership|
|CAC0138||CAC0138||ABC transporter, ATP-binding component (NCBI ptt file)||36, 114|
|CAC0139||CAC0139||Predicted permease (NCBI ptt file)||36, 114|
|CAC0141||CAC0141||Membrane permease, predicted cation efflux pumps (NCBI ptt file)||36, 114|
|CAC0158||glmS||Glucoseamine-fructose-6-phosphate aminotransferase (gene glmS) (NCBI ptt file)||36, 84|
|CAC0300||CAC0300||DNA-polymerase III, gamma subunit (NCBI ptt file)||315, 329|
|CAC0301||CAC0301||Signal peptidase II (PSP1) homolog, YAAT B.subtilis ortholog (NCBI ptt file)||36, 271|
|CAC1429||galE||UDP-glucose 4-epimerase (NCBI ptt file)||271, 329|
|CAC1629||CAC1629||Putative intracellular protease/amidase, ThiJ family (NCBI ptt file)||36, 45|
|CAC1652||aspA||Aspartate ammonia-lyase (NCBI ptt file)||109, 329|
|CAC1686||CAC1686||S-adenosylmethionine-dependent methyltransferase (NCBI ptt file)||315, 329|
|CAC1701||CAC1701||Sensory histidine kinase (with HAMP and PAS domains) (NCBI ptt file)||100, 329|
|CAC1711||CAC1711||Predicted GTPase (NCBI ptt file)||329, 350|
|CAC1718||CAC1718||Guanylate kinase, YLOD B.subtilis ortholog (NCBI ptt file)||3, 329|
|CAC1723||fmt||Methionyl-tRNA formyltransferase (NCBI ptt file)||159, 329|
|CAC1724||CAC1724||Predicted metal-dependent peptidase (NCBI ptt file)||159, 329|
|CAC1726||CAC1726||Predicted Fe-S-cluster redox enzyme, YLON B.subtilis ortholog (NCBI ptt file)||213, 329|
|CAC1728||CAC1728||Serine/threonine protein kinase, Pkn2 family (YLOP B.subtilis ortholog) (NCBI ptt file)||314, 329|
|CAC1730||CAC1730||Pentose-5-phosphate-3-epimerase, YLOR B.subtilis ortholog (NCBI ptt file)||315, 329|
|CAC1734||CAC1734||Uncharacterized, alkaline shock induced protein (NCBI ptt file)||36, 329|
|CAC1735||CAC1735||Predicted kinase related to hydroxyacetone kinase, YLOV ortholog (NCBI ptt file)||36, 335|
|CAC1836||mutL||DNA mismatch repair enzyme, MutL (NCBI ptt file)||36, 159|
|CAC1838||CAC1838||Predicted Fe-S oxidoreductase, YMCB B.subtilis ortholog (NCBI ptt file)||36, 159|
|CAC2233||CAC2233||TRNA 5-methylaminomethyl-2-thiouridylate)-methyltransferase, PP-loop ATPase (NCBI ptt file)||329, 363|
|CAC2234||nifS||NifS family enzyme (cysteine desulfurase/cysteine sulfinate desulfinase) (NCBI ptt file)||51, 329|
|CAC2269||aspS||Aspartyl-tRNA synthetase (NCBI ptt file)||51, 329|
|CAC2565||CAC2565||NifU-related domain containing protein (NCBI ptt file)||36, 153|
|CAC2572||CAC2572||Possible aminoglycoside phosphotransferase (protein kinase related), diverged (NCBI ptt file)||67, 329|
|CAC2629||CAC2629||Hypothetical secreted protein (NCBI ptt file)||36, 310|
|CAC2632||CAC2632||Hypothetical protein (NCBI ptt file)||310, 329|
|CAC2641||tig||FKBP-type peptidyl-prolyl cis-transisomerase (trigger factor) (NCBI ptt file)||304, 329|
|CAC2845||prfB||Protein chain release factor B (NCBI ptt file)||329, 335|
|CAC2846||secA||Preprotein translocase subunit SecA (ATPase, RNA helicase) (NCBI ptt file)||100, 329|
|CAC2858||mreV||Shape-determining protein envB (HSP70 family charepones) (NCBI ptt file)||36, 63|
|CAC2880||CAC2880||Ribose 5-phosphate isomerase, RpiB (NCBI ptt file)||36, 329|
|CAC2895||ddlA||D-alanine-D-alanine ligase (NCBI ptt file)||310, 329|
|CAC3006||CAC3006||Zn-dependent peptidase, insulinase family (NCBI ptt file)||243, 329|
|CAC3017||CAC3017||Predicted xylanase/chitin deacetylase (NCBI ptt file)||36, 335|
|CAC3040||CAC3040||CPSC/CAPB subfamily ATPase (NCBI ptt file)||36, 235|
|CAC3138||fus||Translation elongation factor EF-G (NCBI ptt file)||36, 335|
|CAC3187||CAC3187||Predicted nucleic-acid-binding protein protein, containing HHH domain, YACK B.subtilis ortholog (NCBI ptt file)||36, 329|
|CAC3188||sms||Predicted ATP-dependent serine protease, RADA homolog (NCBI ptt file)||36, 271|
|CAC3708||CAC3708||Hypothetical protein (NCBI ptt file)||36, 44|
|CAC3709||CAC3709||DNA segregation ATPase, FtsK/SpoIIIE family, YUKA B.subtilis ortholog (NCBI ptt file)||36, 44|
|CAC3710||CAC3710||Uncharacterized protein, YUKC B.subtilis homolog (NCBI ptt file)||36, 44|
|CAC3711||CAC3711||Hypothetical protein (NCBI ptt file)||36, 44|
|CAC3716||lonB||Lon-like ATP-dependent protease (NCBI ptt file)||36, 114|
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.
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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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