Organism : Clostridium acetobutylicum | Module List :
CAC0514

CBS domain, similar to B.subtilis ytoI (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Predicted transcriptional regulator containing CBS domains cog/ cog
catalytic activity go/ molecular_function
voltage-gated chloride channel activity go/ molecular_function
chloride transport go/ biological_process
metabolic process go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0514
(Mouseover regulator name to see its description)

CAC0514 is regulated by 18 influences and regulates 15 modules.
Regulators for CAC0514 (18)
Regulator Module Operator
CAC0493 64 tf
CAC0514 64 tf
CAC0929 64 tf
CAC1404 64 tf
CAC2052 64 tf
CAC2473 64 tf
CAC2851 64 tf
CAC2934 64 tf
CAC3166 64 tf
CAC0240 272 tf
CAC0254 272 tf
CAC0289 272 tf
CAC0445 272 tf
CAC0514 272 tf
CAC0707 272 tf
CAC1670 272 tf
CAC1753 272 tf
CAC1945 272 tf

Warning: CAC0514 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
6782 2.30e-03 AGGaGG
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6783 1.20e+04 GCaGcCc
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7196 2.20e+02 gGAaGGCt
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7197 1.30e+03 CACCGC
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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 CAC0514

CAC0514 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Predicted transcriptional regulator containing CBS domains cog/ cog
catalytic activity go/ molecular_function
voltage-gated chloride channel activity go/ molecular_function
chloride transport go/ biological_process
metabolic process go/ biological_process
membrane go/ cellular_component
Module neighborhood information for CAC0514

CAC0514 has total of 47 gene neighbors in modules 64, 272
Gene neighbors (47)
Gene Common Name Description Module membership
CAC0004 recF RecF, ABC family ATPase (NCBI ptt file) 26, 272
CAC0005 CAC0005 Uncharacterized small conserved protein, ortholog of YAAB B.subtilis (NCBI ptt file) 64, 298
CAC0006 gyrB DNA gyrase (topoisomerase II) B subunit (NCBI ptt file) 57, 64
CAC0296 csfB Zn-finger containing protein, csfB B.subtilis homolog (NCBI ptt file) 64, 154
CAC0328 CAC0328 Predicted metal-dependent hydrolase (NCBI ptt file) 72, 272
CAC0493 CAC0493 Uncharcterized small conserved protein, YhhG family (NCBI ptt file) 64, 232
CAC0514 CAC0514 CBS domain, similar to B.subtilis ytoI (NCBI ptt file) 64, 272
CAC0531 CAC0531 Transcriptional regulator, RpiR family (NCBI ptt file) 41, 64
CAC0637 tyrS Tyrosyl-tRNA synthetase (NCBI ptt file) 10, 64
CAC0672 CAC0672 Fision threonyl-tRNA synthetase (N-terminal part) and uridine kinase (NCBI ptt file) 64, 273
CAC0673 CAC0673 L-serine dehydratase, beta chain (NCBI ptt file) 64, 273
CAC0707 rpoN RNA polymerase sigma-54 factor (NCBI ptt file) 170, 272
CAC0904 CAC0904 ATPase with chaperon activity, two ATP-binding domains, ClpC orthologs (NCBI ptt file) 64, 298
CAC1087 CAC1087 Hypothetical protein (NCBI ptt file) 139, 272
CAC1134 CAC1134 Phage related protein, YonF B.subtilis homolog (NCBI ptt file) 195, 272
CAC1137 CAC1137 Hypothetical protein (NCBI ptt file) 30, 272
CAC1295 CAC1295 ERA GTPase (NCBI ptt file) 64, 84
CAC1302 CAC1302 Predicted SAM-dependent methyltransferase (NCBI ptt file) 10, 64
CAC1321 glpK Glycerol kinase, GLPK (NCBI ptt file) 272, 342
CAC1404 CAC1404 Transcriptional regulator of sugar metabolism (deoR family) (NCBI ptt file) 64, 109
CAC1414 CAC1414 TerE family protein, ortholog of stress responce protein SCP2 (YCEC) B.subtilis (NCBI ptt file) 272, 298
CAC1416 CAC1416 Predicted acetyltransferase (NCBI ptt file) 64, 298
CAC1418 CAC1418 Nitroreductase family protein (NCBI ptt file) 57, 272
CAC1477 CAC1477 Hypothetical protein (NCBI ptt file) 272, 301
CAC1622 CAC1622 Pyridoxal kinase related protein (NCBI ptt file) 64, 261
CAC1624 CAC1624 Uncharacterized protein from DegV (B.subtilis) family (NCBI ptt file) 64, 298
CAC1679 CAC1679 Hypothetical protein (NCBI ptt file) 64, 128
CAC1796 CAC1796 Predicted membrane-associated Zn-dependent protease (NCBI ptt file) 64, 91
CAC1849 CAC1849 Predicted flavoprotein, YhiN family (NCBI ptt file) 64, 272
CAC1850 CAC1850 Transcriptional regulators, RpiR family (NCBI ptt file) 64, 211
CAC1851 CAC1851 Predicted pseudouridylate synthase (NCBI ptt file) 64, 211
CAC1857 CAC1857 Predicted metal-dependent peptidase (NCBI ptt file) 57, 64
CAC1858 CAC1858 MoxR-like ATPase (NCBI ptt file) 64, 106
CAC1859 CAC1859 Hypothetical protein (NCBI ptt file) 57, 64
CAC1947 CAC1947 Phage related transcriptional regulator (Xre family) (NCBI ptt file) 270, 272
CAC2052 CAC2052 DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 41, 64
CAC2053 CAC2053 Hypothetical protein (NCBI ptt file) 41, 64
CAC2063 dacF D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 57, 64
CAC2079 CAC2079 Hypothetical protein (NCBI ptt file) 86, 272
CAC2085 CAC2085 Uncharacterized protein from alkaline shock protein family, YQHY B.subtilis ortholog (NCBI ptt file) 64, 273
CAC2474 def N-formylmethionyl-tRNA deformylase (NCBI ptt file) 57, 272
CAC2511 CAC2511 Predicted membrane protein (NCBI ptt file) 272, 320
CAC2665 CAC2665 Xanthosine triphosphate pyrophosphatase, HAM1-like protein (NCBI ptt file) 64, 281
CAC2677 CAC2677 Lytic murein transglycosylase (NCBI ptt file) 64, 298
CAC2805 CAC2805 Possible selenocysteine lyase (aminotransferase of NifS family) (NCBI ptt file) 148, 272
CAC3045 CAC3045 CPSB/CAPC ortholog, PHP family hydrolase (NCBI ptt file) 272, 333
CAC3658 CAC3658 Uncharacterized conserved membrane protein, SapB/MtgC family (NCBI ptt file) 41, 272
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 CAC0514
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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