Organism : Clostridium acetobutylicum | Module List :
CAC1786 codY

Transcriptional regulator, CodY B.subtilis ortholog (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Pleiotropic transcriptional repressor cog/ cog
DNA binding go/ molecular_function
GTP binding go/ molecular_function
transcription repressor activity go/ molecular_function
codY_Gpos tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1786
(Mouseover regulator name to see its description)

CAC1786 is regulated by 22 influences and regulates 20 modules.
Regulators for CAC1786 codY (22)
Regulator Module Operator
CAC0191 251 tf
CAC0197 251 tf
CAC0265 251 tf
CAC0571 251 tf
CAC0768 251 tf
CAC0849 251 tf
CAC1455 251 tf
CAC1467 251 tf
CAC1559 251 tf
CAC1753 251 tf
CAC1786 251 tf
CAC1869 251 tf
CAC2060 251 tf
CAC3409 251 tf
CAC0144 215 tf
CAC0191 215 tf
CAC0849 215 tf
CAC1455 215 tf
CAC1786 215 tf
CAC2060 215 tf
CAC2084 215 tf
CAC3731 215 tf

Warning: CAC1786 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7082 1.60e+01 ggGAgga
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7083 8.10e+02 gTGGAACagc.GAAg
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7154 2.00e+01 gaTGgAAGG.G
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7155 1.10e+04 GGG.ggCc
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for CAC1786

CAC1786 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pleiotropic transcriptional repressor cog/ cog
DNA binding go/ molecular_function
GTP binding go/ molecular_function
transcription repressor activity go/ molecular_function
codY_Gpos tigr/ tigrfam
Module neighborhood information for CAC1786

CAC1786 has total of 44 gene neighbors in modules 215, 251
Gene neighbors (44)
Gene Common Name Description Module membership
CAC0040 CAC0040 Uncharacterized small conserved protein, homolog of yfjA/yukE B.subtilis (NCBI ptt file) 82, 251
CAC0187 nagB Glucosamine-6-phosphate isomerase (glucosamine-6-phosphate deaminase) (gene nagB) (NCBI ptt file) 11, 215
CAC0272 CAC0272 Amino acid transporter (NCBI ptt file) 201, 215
CAC0279 CAC0279 Peptidil-prolyl cis-trans isomerase (NCBI ptt file) 251, 348
CAC0330 CAC0330 Propiloprotein diacylglyceryltransferase (NCBI ptt file) 201, 215
CAC0413 CAC0413 Uncharacterized small conserved protein, homolog of YUKE/YFJA (NCBI ptt file) 242, 251
CAC0506 CAC0506 Penicillin-binding protein (NCBI ptt file) 151, 215
CAC0507 CAC0507 Predicted metal-dependent membrane hydrolase (NCBI ptt file) 151, 215
CAC0510 murB UDP-N-acetylenolpyruvoylglucosamine reductase (murB) (NCBI ptt file) 215, 224
CAC0539 manB Beta-mannanase ManB, contains ChW-repeats (NCBI ptt file) 82, 251
CAC0573 CAC0573 Uncharacterized protein, homolog YvqG B.subtilis (NCBI ptt file) 102, 251
CAC0624 CAC0624 Hypothetical protein (NCBI ptt file) 122, 251
CAC0683 CAC0683 Hypothetical protein (NCBI ptt file) 8, 215
CAC0684 CAC0684 CBS domains (NCBI ptt file) 215, 302
CAC0685 CAC0685 Putative Mn transporter, NRAMP family (NCBI ptt file) 151, 215
CAC0706 CAC0706 Endo-1,4-beta glucanase (fused to two ricin-B-like domains) (NCBI ptt file) 170, 251
CAC0783 CAC0783 Uncharacterized low-complexity protein (NCBI ptt file) 82, 251
CAC0784 CAC0784 ATP-dependent RNA helicase, superfamily II (NCBI ptt file) 82, 251
CAC0806 CAC0806 Hypothetical protein (NCBI ptt file) 218, 251
CAC0819 CAC0819 Phosphoribosylpyrophosphate synthetase (NCBI ptt file) 215, 251
CAC1083 CAC1083 Predicted membrane-associated metal-binding protein (NCBI ptt file) 185, 251
CAC1234 pheB Chorismate mutase PheB of B.subtilis ortholog (NCBI ptt file) 76, 215
CAC1241 radc RadC protein ortholog (NCBI ptt file) 3, 251
CAC1272 CAC1272 Predicted membrane protein (NCBI ptt file) 106, 215
CAC1301 CAC1301 Predicted membrane protein (NCBI ptt file) 10, 251
CAC1620 CAC1620 Small acid-soluble spore protein (NCBI ptt file) 251, 265
CAC1716 CAC1716 Uncharacterized stress-induced protein, YicC family (NCBI ptt file) 3, 251
CAC1753 CAC1753 Uncharacterized conserved protein, YLXM B.subtilis ortholog (NCBI ptt file) 251, 302
CAC1754 ffh Signal recognition particle GTPase Ffh (NCBI ptt file) 251, 302
CAC1786 codY Transcriptional regulator, CodY B.subtilis ortholog (NCBI ptt file) 215, 251
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
CAC2244 CAC2244 HAD superfamily hydrolases, YKRA B.subtilis ortholog (NCBI ptt file) 216, 251
CAC2276 CAC2276 Protein related to N-terminal domain of SS-DNA-specific exonuclease RecJ (NCBI ptt file) 215, 327
CAC2324 CAC2324 Glycosyltransferase (NCBI ptt file) 82, 215
CAC2564 CAC2564 Hypothetical protein (NCBI ptt file) 153, 215
CAC3034 CAC3034 MutS-like mismatch repair protein, ATPases (NCBI ptt file) 11, 215
CAC3062 CAC3062 CPSB/CAPC ortholog, PHP family hydrolase (NCBI ptt file) 238, 251
CAC3092 231 amidase, germination specific (cwlC/cwlD B.subtilis ortholog) (NCBI ptt file) 160, 215
CAC3195 CAC3195 Glycyl-tRNA synthetase (NCBI ptt file) 90, 215
CAC3210 CAC3210 Predicted RNA-binding protein, YABO B.subtilis ortholog (NCBI ptt file) 215, 281
CAC3221 prs Phosphoribosylpyrophosphate synthetase (NCBI ptt file) 109, 251
CAC3539 murA UDP-N-acetylglucosamine enolpyruvyl transferase (NCBI ptt file) 215, 350
CAC3668 CAC3668 MDR-type permease (NCBI ptt file) 82, 251
Gene Page Help

Network Tab

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.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

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.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

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.

Functions Tab

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.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our 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
  • 6. Visualisation legend
Comments for CAC1786
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our 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
  • 6. Visualisation legend