Organism : Clostridium acetobutylicum | Module List :
CAC2818

AraC-type DNA-binding domain-containing protein, transcriptional regulator (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2818
(Mouseover regulator name to see its description)

CAC2818 is regulated by 20 influences and regulates 7 modules.
Regulators for CAC2818 (20)
Regulator Module Operator
CAC0289 223 tf
CAC0599 223 tf
CAC1046 223 tf
CAC2074 223 tf
CAC2486 223 tf
CAC2568 223 tf
CAC2818 223 tf
CAC2889 223 tf
CAC3271 223 tf
CAC3472 223 tf
CAC3525 223 tf
CAC0189 241 tf
CAC0445 241 tf
CAC0493 241 tf
CAC0599 241 tf
CAC2471 241 tf
CAC2495 241 tf
CAC2768 241 tf
CAC2939 241 tf
CAC3429 241 tf

Warning: CAC2818 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
7098 5.70e+03 GGAcCG
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7099 5.30e+00 CacCTcta
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7134 3.90e+03 aGGAgaGa
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7135 2.30e-01 t.aAGG.G
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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 CAC2818

CAC2818 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
AraC-type DNA-binding domain-containing proteins cog/ cog
DNA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for CAC2818

CAC2818 has total of 40 gene neighbors in modules 223, 241
Gene neighbors (40)
Gene Common Name Description Module membership
CAC0080 agrC Histidine kinase-like ATPase (NCBI ptt file) 137, 241
CAC0101 CAC0101 Methyl-accepting chemotaxis protein (NCBI ptt file) 241, 333
CAC0123 CAC0123 Cytosine deaminase (NCBI ptt file) 30, 223
CAC0167 CAC0167 Possible sigma factor, diverged member of sigF/sigE/sigG family (NCBI ptt file) 191, 223
CAC0189 CAC0189 Similar to transcriptional regulator, GntR family (NCBI ptt file) 241, 343
CAC0271 CAC0271 Predicted esterase (NCBI ptt file) 49, 241
CAC0373 CAC0373 ABC transporter, ATP binding protein (NCBI ptt file) 171, 241
CAC0463 CAC0463 Serine protease Do (heat-shock protein) (NCBI ptt file) 207, 223
CAC0541 CAC0541 SAM-dependent methyltransferase (NCBI ptt file) 185, 223
CAC0599 CAC0599 Transcriptional regulator, GntR family (NCBI ptt file) 223, 291
CAC0608 lisA Diaminopimelate decarboxilase, lisA (NCBI ptt file) 202, 223
CAC0720 CAC0720 Hypothetical protein (NCBI ptt file) 223, 240
CAC0736 CAC0736 Possible glucanotransferase (putative endo alpha-1,4 polygalactosaminidase related protein) (NCBI ptt file) 28, 241
CAC0757 CAC0757 Predicted membrane protein (NCBI ptt file) 70, 223
CAC0854 tet Tetracycline resistance protein tetP, contain GTP-ase domain (NCBI ptt file) 241, 316
CAC0855 CAC0855 Predicted phosphatase (NCBI ptt file) 72, 241
CAC0887 adeC Adenine deaminase (NCBI ptt file) 65, 241
CAC1631 CAC1631 Biotin synthase family enzyme (NCBI ptt file) 137, 241
CAC2557 CAC2557 Hypothetical protein (NCBI ptt file) 223, 349
CAC2568 CAC2568 Predicted transcriptional regulator (NCBI ptt file) 71, 223
CAC2768 CAC2768 Transcriptional regulators, AcrR family (NCBI ptt file) 241, 333
CAC2816 CAC2816 Hypothetical protein, CF-17 family (NCBI ptt file) 241, 333
CAC2818 CAC2818 AraC-type DNA-binding domain-containing protein, transcriptional regulator (NCBI ptt file) 223, 241
CAC2930 CAC2930 Uncharacterized conserved membrane protein (NCBI ptt file) 71, 223
CAC2931 CAC2931 Uncharacterized conserved membrane protein (NCBI ptt file) 71, 223
CAC2932 CAC2932 ABC-type MDR transporter, ATPase component (NCBI ptt file) 223, 349
CAC3000 CAC3000 Hypothetical protein (NCBI ptt file) 92, 223
CAC3027 CAC3027 Predicted phosphohydrolase (NCBI ptt file) 216, 223
CAC3121 rplE Ribosomal protein L5 (NCBI ptt file) 59, 241
CAC3238 CAC3238 Ucharacterized Fe-S oxidoreductase (NCBI ptt file) 125, 241
CAC3271 CAC3271 Transcriptional regulator, AcrR family (NCBI ptt file) 223, 285
CAC3276 nrdB Ribonucleotide reductase beta subunit (NCBI ptt file) 141, 241
CAC3381 CAC3381 Membrane protease subunit, stomatin/prohibitin homolog (NCBI ptt file) 15, 223
CAC3429 CAC3429 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 220, 241
CAC3471 CAC3471 GMP reductase (NCBI ptt file) 223, 301
CAC3493 CAC3493 Predicted transcriptional regulator component, YOBU B.subtilis homolog (NCBI ptt file) 137, 241
CAC3525 CAC3525 Uncharacterized conserved protein, YjeB/RRF2 family (NCBI ptt file) 223, 349
CAC3532 CAC3532 Hypothetical protein (NCBI ptt file) 241, 333
CAC3645 CAC3645 CRO repressor-like DNA-binding protein (NCBI ptt file) 120, 241
CAC3733 gidA Glucose-inhibited division protein, GIDA (NAD/FAD-utilizing enzyme) (NCBI ptt file) 120, 241
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 CAC2818
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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