Organism : Clostridium acetobutylicum | Module List :
CAC0402

Possible transcriptional regulatory protein, AsnC family (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0402
(Mouseover regulator name to see its description)

CAC0402 is regulated by 18 influences and regulates 21 modules.
Regulators for CAC0402 (18)
Regulator Module Operator
CAC0183 125 tf
CAC0402 125 tf
CAC0445 125 tf
CAC0599 125 tf
CAC0951 125 tf
CAC0977 125 tf
CAC2471 125 tf
CAC2818 125 tf
CAC3472 125 tf
CAC0189 333 tf
CAC0402 333 tf
CAC0951 333 tf
CAC1668 333 tf
CAC1915 333 tf
CAC2471 333 tf
CAC2768 333 tf
CAC2939 333 tf
CAC3472 333 tf

Warning: CAC0402 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
6902 1.70e+01 CcTcCT
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6903 1.00e+03 gGtt.agtaG.gatgatgAg
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7318 1.80e+02 ggAG.gG
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7319 9.60e+02 TtAaGGaGgAc
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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 CAC0402

Warning: No Functional annotations were found!

Module neighborhood information for CAC0402

CAC0402 has total of 35 gene neighbors in modules 125, 333
Gene neighbors (35)
Gene Common Name Description Module membership
CAC0039 CAC0039 DNA segregation ATPase FtsK/SpoIIIE family protein, contains FHA domain (NCBI ptt file) 258, 333
CAC0048 CAC0048 Hypothetical protein, CF-17 family (NCBI ptt file) 264, 333
CAC0101 CAC0101 Methyl-accepting chemotaxis protein (NCBI ptt file) 241, 333
CAC0363 CAC0363 Deoxyinosine 3'endonuclease (NCBI ptt file) 333, 347
CAC0364 CAC0364 Metal-dependent hydrolases of the metallobeta-lactamase superfamily (NCBI ptt file) 141, 333
CAC0402 CAC0402 Possible transcriptional regulatory protein, AsnC family (NCBI ptt file) 125, 333
CAC0622 CAC0622 Polyphosphate kinase (NCBI ptt file) 125, 145
CAC0782 CAC0782 Hypothetical protein (NCBI ptt file) 125, 257
CAC0811 CAC0811 Hydrogenase expression-formation factor (hypD) (NCBI ptt file) 78, 125
CAC0927 CAC0927 Hypothetical protein, CF-2 family (NCBI ptt file) 46, 125
CAC0960 CAC0960 Predicted xylanase related protein (NCBI ptt file) 125, 307
CAC1431 rpiA Ribose 5-phosphate isomerase (NCBI ptt file) 125, 127
CAC1457 CAC1457 PTS system, fructose(mannose)-specific IIA component (NCBI ptt file) 125, 136
CAC1961 CAC1961 Predicted phosphohydrolases, Icc family (NCBI ptt file) 125, 257
CAC2029 CAC2029 Hypothetical protein (NCBI ptt file) 141, 333
CAC2044 CAC2044 Hypothetical protein (NCBI ptt file) 141, 333
CAC2101 CAC2101 Hypothetical protein (NCBI ptt file) 54, 333
CAC2109 CAC2109 Acetyltransferase (NCBI ptt file) 125, 148
CAC2702 CAC2702 Possible signal transduction protein (containing EAL, CBS and GGDEF domains) (NCBI ptt file) 123, 333
CAC2748 deaD ATP dependent RNA helicase DeaD, superfamily II (NCBI ptt file) 59, 333
CAC2766 CAC2766 Thiamine biosynthesis lipoprotein ApbE (NCBI ptt file) 46, 333
CAC2768 CAC2768 Transcriptional regulators, AcrR family (NCBI ptt file) 241, 333
CAC2792 CAC2792 Uncharcterized conserved membrane protein, YXAI B.subtilis homolog (NCBI ptt file) 148, 333
CAC2816 CAC2816 Hypothetical protein, CF-17 family (NCBI ptt file) 241, 333
CAC3045 CAC3045 CPSB/CAPC ortholog, PHP family hydrolase (NCBI ptt file) 272, 333
CAC3238 CAC3238 Ucharacterized Fe-S oxidoreductase (NCBI ptt file) 125, 241
CAC3257 CAC3257 Predicted membrane protein (NCBI ptt file) 137, 333
CAC3358 CAC3358 Site-specific DNA methylase dam (NCBI ptt file) 125, 171
CAC3367 CAC3367 Protein distantly similar to N-terminal fragment of HSP60 chaperonin family (NCBI ptt file) 125, 171
CAC3431 CAC3431 Membrane export protein, related to SecD/SecF protein exporters (NCBI ptt file) 141, 333
CAC3432 CAC3432 Alpha/beta superfamily hydrolase (NCBI ptt file) 141, 333
CAC3506 CAC3506 Predicted MDR-type permease (NCBI ptt file) 43, 125
CAC3532 CAC3532 Hypothetical protein (NCBI ptt file) 241, 333
CAC3689 CAC3689 Uncharacterized conserved protein, phnB family (NCBI ptt file) 125, 333
CAC3690 CAC3690 Uncharacterized conserved protein, related to polyketide cyclase (CypC) (NCBI ptt file) 78, 125
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 CAC0402
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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