Organism : Clostridium acetobutylicum | Module List :
CAC0289

Response regulator (CheY domain, HTH domain) (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
protein-glutamate methylesterase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0289
(Mouseover regulator name to see its description)

CAC0289 is regulated by 18 influences and regulates 33 modules.
Regulators for CAC0289 (18)
Regulator Module Operator
CAC0078 94 tf
CAC0191 94 tf
CAC0265 94 tf
CAC0289 94 tf
CAC0550 94 tf
CAC1451 94 tf
CAC1467 94 tf
CAC1696 94 tf
CAC3046 94 tf
CAC3409 94 tf
CAC0078 212 tf
CAC0191 212 tf
CAC0289 212 tf
CAC0550 212 tf
CAC0681 212 tf
CAC1467 212 tf
CAC1695 212 tf
CAC1869 212 tf

Warning: CAC0289 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
6842 3.60e-06 CCcCCT
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6843 3.90e+03 CaGGGC
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7076 2.80e-03 GGAGGa
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7077 3.20e+03 Tgctt.aCaAaTa.ta.ga.AaaC
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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 CAC0289

CAC0289 is enriched for 6 functions in 3 categories.
Module neighborhood information for CAC0289

CAC0289 has total of 25 gene neighbors in modules 94, 212
Gene neighbors (25)
Gene Common Name Description Module membership
CAC0069 CAC0069 Predicted iron-binding protein, hemerythrin (NCBI ptt file) 212, 253
CAC0118 cheA Chemotaxis protein cheA (NCBI ptt file) 94, 107
CAC0251 CAC0251 Uncharacterized Fe-S protein (fragment) (NCBI ptt file) 165, 212
CAC0289 CAC0289 Response regulator (CheY domain, HTH domain) (NCBI ptt file) 94, 212
CAC0403 CAC0403 Secreted protein contains fibronectin type III domains (NCBI ptt file) 94, 242
CAC0551 CAC0551 Uncharacterized protein with possible cell attachment and effacing function; Cell-adhesion domain (NCBI ptt file) 94, 212
CAC0731 CAC0731 FUSION: Nucleoside-diphosphate-sugar epimerase and GAF domain (NCBI ptt file) 94, 212
CAC0732 CAC0732 Predicted membrane protein (NCBI ptt file) 94, 212
CAC0733 CAC0733 Predicted membrane protein (NCBI ptt file) 94, 212
CAC0734 CAC0734 Glycosyltransferases I (lipopolysaccharide biosynthesis protein-related protein) (NCBI ptt file) 94, 212
CAC0796 CAC0796 CDP-diglyceride synthetase (NCBI ptt file) 212, 218
CAC0797 CAC0797 Phosphoenolpyruvate synthase (NCBI ptt file) 202, 212
CAC0801 CAC0801 Phosphoenolpyruvate synthase (NCBI ptt file) 94, 212
CAC0802 CAC0802 Hypothetical protein (NCBI ptt file) 212, 353
CAC0848 CAC0848 Uncharacterized conserved protein, YitT family (NCBI ptt file) 90, 212
CAC0909 CAC0909 Methyl-accepting chemotaxis protein, contain HAMP domain (NCBI ptt file) 90, 94
CAC1067 CAC1067 TPR-repeat containing protein (NCBI ptt file) 94, 327
CAC2483 CAC2483 Methyl-accepting chemotaxis protein (NCBI ptt file) 94, 212
CAC2521 CAC2521 Hypothetical protein, CF-41 family (NCBI ptt file) 94, 216
CAC2548 CAC2548 Reductase/isomerase/elongation factor common domain (NCBI ptt file) 94, 202
CAC2837 CAC2837 Fusion HD-GYP domain and HD-hydrolase domain (NCBI ptt file) 212, 216
CAC3335 CAC3335 Short-chain alcohol dehydrogenase family enzyme (NCBI ptt file) 212, 356
CAC3336 CAC3336 Predicted cAMP-binding domain, regulatory protein, diverged (NCBI ptt file) 212, 356
CAC3505 CAC3505 Multimeric flavodoxin WrbA family protein (NCBI ptt file) 212, 291
CAC3510 CAC3510 Membrane associated methyl-accepting chemotaxis protein (with HAMP domain) (NCBI ptt file) 94, 212
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 CAC0289
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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