Organism : Clostridium acetobutylicum | Module List :
CAC2546

Transcriptional regulator, FadR family (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA 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
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2546
(Mouseover regulator name to see its description)

CAC2546 is regulated by 19 influences and regulates 19 modules.
Regulators for CAC2546 (19)
Regulator Module Operator
CAC0162 276 tf
CAC0821 276 tf
CAC0876 276 tf
CAC1668 276 tf
CAC1766 276 tf
CAC1800 276 tf
CAC2546 276 tf
CAC0197 185 tf
CAC0465 185 tf
CAC0745 185 tf
CAC0860 185 tf
CAC1046 185 tf
CAC1800 185 tf
CAC2473 185 tf
CAC3349 185 tf
CAC3481 185 tf
CAC3509 185 tf
CAC3525 185 tf
CAC3687 185 tf

Warning: CAC2546 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
7022 7.10e+03 CAGGCC
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7023 7.20e+01 gGAtTaTAagggggaGgcgT
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7204 1.70e-02 aGGaggaA
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7205 2.70e+01 TaAgacaGaaGAGGT
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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 CAC2546

CAC2546 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA 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
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for CAC2546

CAC2546 has total of 42 gene neighbors in modules 185, 276
Gene neighbors (42)
Gene Common Name Description Module membership
CAC0055 CAC0055 Uncharacterized predicted metal-binding protein, ortholog of Streptomyces (2808777) (NCBI ptt file) 71, 185
CAC0094 CAC0094 Ferredoxin-nitrite reductase (NCBI ptt file) 27, 276
CAC0160 CAC0160 Predicted acetyltransferase (NCBI ptt file) 185, 345
CAC0162 CAC0162 Transcriptional regulator MarR/EmrR family (NCBI ptt file) 83, 276
CAC0239 CAC0239 Histidine kinase-like ATPase (NCBI ptt file) 185, 346
CAC0268 CAC0268 ABC transporter ATP-binding protein (NCBI ptt file) 27, 276
CAC0269 CAC0269 Uncharacterized membrane protein (NCBI ptt file) 27, 276
CAC0292 CAC0292 Hypothetical protein (NCBI ptt file) 162, 276
CAC0417 CAC0417 Similar to arsenate reductase (NCBI ptt file) 71, 185
CAC0420 CAC0420 Conserved membrane protein, possible homolog of CAAX-like membrane endopeptidase (NCBI ptt file) 185, 247
CAC0515 CAC0515 Uncharacterized conserved protein (NCBI ptt file) 25, 276
CAC0541 CAC0541 SAM-dependent methyltransferase (NCBI ptt file) 185, 223
CAC0597 gerKB Spore germination protein, gerKB (NCBI ptt file) 115, 185
CAC0747 CAC0747 Secreted protein containing uncharacterized conserved protein of ErfK family (NCBI ptt file) 49, 185
CAC0851 CAC0851 Ortholog ygiD E.coli (NCBI ptt file) 167, 185
CAC0860 CAC0860 Two-component response regulator (NCBI ptt file) 185, 206
CAC0954 CAC0954 Uncharacterized membrane protein (NCBI ptt file) 25, 276
CAC1028 CAC1028 Hydrolase of alpha/beta superfamily, possible membrane associated lipase (NCBI ptt file) 276, 356
CAC1040 CAC1040 Predicted amidohydrolases (NCBI ptt file) 185, 346
CAC1050 nadE NH(3)-dependent NAD(+) synthetase (NCBI ptt file) 31, 276
CAC1083 CAC1083 Predicted membrane-associated metal-binding protein (NCBI ptt file) 185, 251
CAC1434 CAC1434 Alkaline phosphatase superfamily protein (NCBI ptt file) 176, 276
CAC1490 CAC1490 Hypothetical protein (NCBI ptt file) 185, 259
CAC1491 CAC1491 Predicted ATPase (NCBI ptt file) 146, 185
CAC1557 CAC1557 Predicted acetyltransferase (NCBI ptt file) 1, 185
CAC1581 CAC1581 Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) 185, 259
CAC1670 CAC1670 Response regulator (CheY-like receiver domain and DNA-binding HTH domain) (NCBI ptt file) 185, 326
CAC1683 CAC1683 Predicted metal-dependent hydrolase of metallo-beta-lactamase superfamily (NCBI ptt file) 239, 276
CAC1970 CAC1970 Hypothetical protein (NCBI ptt file) 185, 326
CAC2275 apt Adenine phosphoribosyltransferase; Apt (NCBI ptt file) 152, 276
CAC2475 CAC2475 Possible 5-Nitroimidazole antibiotics resistance protein, NimA-family (NCBI ptt file) 261, 276
CAC2546 CAC2546 Transcriptional regulator, FadR family (NCBI ptt file) 185, 276
CAC2759 CAC2759 Response regulator (CheY receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 71, 185
CAC2999 CAC2999 Hypothetical protein (NCBI ptt file) 52, 276
CAC3001 CAC3001 Uncharacterized consrved protein, containing Zn finger (NCBI ptt file) 1, 276
CAC3321 CAC3321 Uncharacterized protein homolog of yveG B.subtilis (NCBI ptt file) 185, 216
CAC3347 CAC3347 Amino acid transporter, permease (NCBI ptt file) 207, 276
CAC3348 CAC3348 Possible homocysteine S-methyltransferase (NCBI ptt file) 157, 276
CAC3435 CAC3435 Hypothetical protein (NCBI ptt file) 185, 359
CAC3580 CAC3580 Dioxygenase related to 2-nitropropane dioxygenase (NCBI ptt file) 31, 276
CAC3581 CAC3581 HAD superfamily hydrolase (NCBI ptt file) 185, 289
CAC3656 CAC3656 Uncharacterized conserved protein, yaiN/yohL family (NCBI ptt file) 185, 291
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 CAC2546
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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