Organism : Clostridium acetobutylicum | Module List :
CAC3429

Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
protein-glutamate methylesterase activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3429
(Mouseover regulator name to see its description)

CAC3429 is regulated by 19 influences and regulates 21 modules.
Regulators for CAC3429 (19)
Regulator Module Operator
CAC0284 220 tf
CAC0289 220 tf
CAC0445 220 tf
CAC0599 220 tf
CAC1467 220 tf
CAC1945 220 tf
CAC3283 220 tf
CAC3429 220 tf
CAC3472 220 tf
CAC3525 220 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: CAC3429 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
7092 1.50e-07 gGGaGG
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7093 2.10e+03 CaCTccaaaCTGtAGTGGaGG
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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 CAC3429

CAC3429 is enriched for 8 functions in 3 categories.
Module neighborhood information for CAC3429

CAC3429 has total of 37 gene neighbors in modules 220, 241
Gene neighbors (37)
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
CAC0189 CAC0189 Similar to transcriptional regulator, GntR family (NCBI ptt file) 241, 343
CAC0245 CAC0245 ABC transporter ATP-binding protein (NCBI ptt file) 154, 220
CAC0261 nifV Homocitrate synthase,alpha subunit nifV(nioA) (NCBI ptt file) 171, 220
CAC0271 CAC0271 Predicted esterase (NCBI ptt file) 49, 241
CAC0373 CAC0373 ABC transporter, ATP binding protein (NCBI ptt file) 171, 241
CAC0521 CAC0521 Hypothetical protein (NCBI ptt file) 177, 220
CAC0645 CAC0645 Similar to spore germination protein (NCBI ptt file) 171, 220
CAC0736 CAC0736 Possible glucanotransferase (putative endo alpha-1,4 polygalactosaminidase related protein) (NCBI ptt file) 28, 241
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
CAC1120 CAC1120 Phage-related protein, YqbO B.subtilis homolog (NCBI ptt file) 104, 220
CAC1547 trxA Thioredoxin, trx (NCBI ptt file) 30, 220
CAC1631 CAC1631 Biotin synthase family enzyme (NCBI ptt file) 137, 241
CAC2534 CAC2534 HD_GYP hydrolase domain fused to HD hydrolase domain (NCBI ptt file) 171, 220
CAC2618 CAC2618 Hypothetical protein, CF-17 family (NCBI ptt file) 171, 220
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
CAC3121 rplE Ribosomal protein L5 (NCBI ptt file) 59, 241
CAC3238 CAC3238 Ucharacterized Fe-S oxidoreductase (NCBI ptt file) 125, 241
CAC3268 CAC3268 Uncharacterized conserved membrane protein, possible MDR-type transporter (NCBI ptt file) 220, 230
CAC3276 nrdB Ribonucleotide reductase beta subunit (NCBI ptt file) 141, 241
CAC3419 CAC3419 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 220, 357
CAC3429 CAC3429 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 220, 241
CAC3446 CAC3446 Predicted epimerase, PhzC/PhzF homolog (NCBI ptt file) 30, 220
CAC3458 CAC3458 Uncharacterized protein, homolog of B. anthracis (gi:48942631) (NCBI ptt file) 30, 220
CAC3462 fabG 3-oxoacyl-acyl carrier protein reductase (NCBI ptt file) 171, 220
CAC3493 CAC3493 Predicted transcriptional regulator component, YOBU B.subtilis homolog (NCBI ptt file) 137, 241
CAC3513 CAC3513 Hypothetical protein (NCBI ptt file) 171, 220
CAC3532 CAC3532 Hypothetical protein (NCBI ptt file) 241, 333
CAC3564 aspC aspartyl-tRNA synthetase (RefSeq) 171, 220
CAC3641 CAC3641 Oligopeptide ABC transporter, ATPase component (NCBI ptt file) 120, 220
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 CAC3429
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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