Organism : Clostridium acetobutylicum | Module List :
CAC2939

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 CAC2939
(Mouseover regulator name to see its description)

CAC2939 is regulated by 27 influences and regulates 9 modules.
Regulators for CAC2939 (27)
Regulator Module Operator
CAC0265 351 tf
CAC1766 351 tf
CAC1843 351 tf
CAC2074 351 tf
CAC2259 351 tf
CAC2793 351 tf
CAC2939 351 tf
CAC3267 351 tf
CAC3406 351 tf
CAC3413 351 tf
CAC0284 258 tf
CAC1032 258 tf
CAC1668 258 tf
CAC1682 258 tf
CAC1770 258 tf
CAC2254 258 tf
CAC2768 258 tf
CAC2939 258 tf
CAC3143 258 tf
CAC3199 258 tf
CAC3216 258 tf
CAC3361 258 tf
CAC3370 258 tf
CAC3399 258 tf
CAC3429 258 tf
CAC3433 258 tf
CAC3502 258 tf

Warning: CAC2939 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
7168 5.80e-10 cCCTCC
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7169 7.50e+03 GCaTGGGC
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7354 5.40e+00 gGaGGa
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7355 1.00e+04 CCGcAAGaG
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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 CAC2939

CAC2939 is enriched for 8 functions in 3 categories.
Module neighborhood information for CAC2939

CAC2939 has total of 51 gene neighbors in modules 258, 351
Gene neighbors (51)
Gene Common Name Description Module membership
CAC0038 CAC0038 Hypothetical protein (NCBI ptt file) 44, 258
CAC0039 CAC0039 DNA segregation ATPase FtsK/SpoIIIE family protein, contains FHA domain (NCBI ptt file) 258, 333
CAC0223 CAC0223 Predicted N6-adenine-specific DNA methylase (NCBI ptt file) 65, 258
CAC0250 CAC0250 Methyl-accepting chemotaxis protein (NCBI ptt file) 207, 258
CAC0343 CAC0343 Hypothetical protein, CF-23 family (NCBI ptt file) 190, 258
CAC0349 CAC0349 Predicted membrane protein (NCBI ptt file) 246, 351
CAC0355 CAC0355 Putative polygalacturonase (pectinase) (NCBI ptt file) 100, 258
CAC0399 CAC0399 Hypothetical protein, CF-24 family (NCBI ptt file) 258, 264
CAC0410 CAC0410 Uncharacterized small conserved protein, homolog of YUKE/YFJA (NCBI ptt file) 258, 264
CAC0419 CAC0419 Predicted membrane protein (NCBI ptt file) 247, 351
CAC0477 CAC0477 AP superfamily (NCBI ptt file) 247, 258
CAC0485 CAC0485 TRNA-processing ribonuclease BN (NCBI ptt file) 137, 258
CAC0509 CAC0509 PHP family protein (NCBI ptt file) 44, 258
CAC0568 asd Aspartate semialdehyde dehydrogenase (gene asd) (NCBI ptt file) 26, 258
CAC0698 CAC0698 Predicted hydrolase of the HAD superfamily (NCBI ptt file) 217, 351
CAC0864 CAC0864 Histidine kinase-like ATPase (NCBI ptt file) 65, 258
CAC0991 CAC0991 Putative intracellular protease (NCBI ptt file) 254, 258
CAC1060 CAC1060 Predicted membrane protein (NCBI ptt file) 336, 351
CAC1064 CAC1064 TPR-repeat-containing protein (NCBI ptt file) 49, 351
CAC1163 CAC1163 Hypothetical protein (NCBI ptt file) 16, 351
CAC1167 CAC1167 Hypothetical protein (NCBI ptt file) 246, 351
CAC1213 CAC1213 Predicted membrane protein (NCBI ptt file) 246, 351
CAC1256 CAC1256 Ribonucleases G/E family protein (NCBI ptt file) 84, 258
CAC1409 CAC1409 Predicted membrane protein (NCBI ptt file) 78, 351
CAC1500 CAC1500 Predicted membrane protein (NCBI ptt file) 13, 351
CAC1517 CAC1517 Membrane associated sensory transduction histidine kinase (NCBI ptt file) 140, 351
CAC1848 cmk Cytidylate kinase (NCBI ptt file) 35, 351
CAC1954 CAC1954 Hypothetical protein (NCBI ptt file) 22, 258
CAC1972 CAC1972 Predicted membrane protein (NCBI ptt file) 191, 351
CAC2032 CAC2032 Hypothetical protein (NCBI ptt file) 3, 258
CAC2168 CAC2168 Uncharacterized conserved protein (NCBI ptt file) 258, 345
CAC2188 CAC2188 Protein containing a domain related to multimeric flavodoxin WrbA family (NCBI ptt file) 351, 355
CAC2259 CAC2259 Predicted transcriptional regulator of MarR-family (NCBI ptt file) 270, 351
CAC2322 CAC2322 Hypothetical protein (NCBI ptt file) 4, 351
CAC2341 CAC2341 Collagenase family protease (NCBI ptt file) 51, 351
CAC2495 CAC2495 Predicted transcriptional regulator (NCBI ptt file) 258, 326
CAC2547 CAC2547 Possible membrane-associated methyl-accepting chemotaxis protein fused to HAMP domain (NCBI ptt file) 145, 258
CAC2550 CAC2550 Hypothetical protein (NCBI ptt file) 3, 258
CAC2559 CAC2559 Hypothetical protein (NCBI ptt file) 183, 351
CAC2566 CAC2566 Possible rRNA methylase (SAM-dependent methyltransferase superfamily), YTQB B.subtilis (NCBI ptt file) 58, 351
CAC2698 CAC2698 Hypothetical protein (NCBI ptt file) 5, 351
CAC2811 CAC2811 Hypothetical protein, CF-17 family (NCBI ptt file) 123, 258
CAC2823 CAC2823 Hypothetical protein (NCBI ptt file) 258, 341
CAC2900 splB Spore photoproduct lyase, SPL related protein (NCBI ptt file) 132, 351
CAC2901 CAC2901 Predicted membrane protein (NCBI ptt file) 298, 351
CAC2939 CAC2939 Response regulator (CheY-like receiver domain and HTH-type DNA-binding domain) (NCBI ptt file) 258, 351
CAC3003 thyA Thymidylate synthase (NCBI ptt file) 100, 258
CAC3004 folA Dihydrofolate reductase (NCBI ptt file) 255, 258
CAC3277 nrdA Ribonucleotide reductase alpha subunit (NCBI ptt file) 244, 258
CAC3391 CAC3391 Membrane associated signal transduction histidine kinase (NCBI ptt file) 51, 351
CAC3404 CAC3404 Uncharactecterized conserved membrane protein, possible ABC-type MDR permease (NCBI ptt file) 246, 351
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 CAC2939
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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