Organism : Clostridium acetobutylicum | Module List :
CAC3421

Acyl carrier protein phosphodiesterase (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Acyl carrier protein phosphodiesterase cog/ cog
electron transport go/ biological_process
[acyl-carrier-protein] phosphodiesterase activity go/ molecular_function
oxidoreductase activity go/ molecular_function
coenzyme binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3421
(Mouseover regulator name to see its description)

CAC3421 is regulated by 19 influences and regulates 0 modules.
Regulators for CAC3421 (19)
Regulator Module Operator
CAC0255 245 tf
CAC1766 245 tf
CAC2471 245 tf
CAC2793 245 tf
CAC3166 245 tf
CAC3603 245 tf
CAC0284 177 tf
CAC0402 177 tf
CAC1430 177 tf
CAC1536 177 tf
CAC1668 177 tf
CAC1941 177 tf
CAC2236 177 tf
CAC2793 177 tf
CAC2794 177 tf
CAC3214 177 tf
CAC3475 177 tf
CAC3611 177 tf
CAC3677 177 tf

Warning: CAC3421 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
7006 6.00e+00 aGgaGgagaAa
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7007 1.60e+04 cAAAGcACC
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7142 1.40e-02 gaGGaG.gAA
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7143 1.20e+04 cGCCaAC
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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 CAC3421

CAC3421 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Acyl carrier protein phosphodiesterase cog/ cog
electron transport go/ biological_process
[acyl-carrier-protein] phosphodiesterase activity go/ molecular_function
oxidoreductase activity go/ molecular_function
coenzyme binding go/ molecular_function
Module neighborhood information for CAC3421

CAC3421 has total of 30 gene neighbors in modules 177, 245
Gene neighbors (30)
Gene Common Name Description Module membership
CAC0166 CAC0166 Uncharacterized conserved protein (NCBI ptt file) 177, 245
CAC0397 CAC0397 Predicted sugar phosphate aminotransferase involved in capsule formation (NCBI ptt file) 136, 245
CAC0455 CAC0455 Hypothetical protein (NCBI ptt file) 95, 177
CAC0466 CAC0466 Hypothetical protein (NCBI ptt file) 78, 177
CAC0468 CAC0468 HAD superfamily hydrolase (NCBI ptt file) 78, 177
CAC0521 CAC0521 Hypothetical protein (NCBI ptt file) 177, 220
CAC0643 CAC0643 Putative spore germination protein (NCBI ptt file) 136, 245
CAC0934 CAC0934 Hypothetical protein (NCBI ptt file) 62, 177
CAC1268 comEA Competence ComEA protein (NCBI ptt file) 243, 245
CAC1421 CAC1421 Pyruvate-formate lyase-activating enzyme (NCBI ptt file) 188, 245
CAC1473 CAC1473 Proline/glycine betaine ABC-type transport system, permease component (NCBI ptt file) 39, 177
CAC1474 CAC1474 Proline/glycine betaine ABC transport system, periplasmic component (NCBI ptt file) 41, 177
CAC1475 CAC1475 Proline/glycine betaine ABC transport system, ATPase component (NCBI ptt file) 41, 177
CAC1505 CAC1505 Hypothetical protein (NCBI ptt file) 245, 257
CAC1594 rpsD Ribosomal protein S4 (NCBI ptt file) 78, 177
CAC1616 CAC1616 Hypothetical protein (NCBI ptt file) 188, 245
CAC1705 CAC1705 Periplasmic phosphate-binding protein (NCBI ptt file) 245, 337
CAC1706 CAC1706 Phosphate permease (NCBI ptt file) 118, 245
CAC1707 CAC1707 Permease component of ATP-dependent phosphate uptake system (NCBI ptt file) 118, 245
CAC1708 CAC1708 ATPase component of ABC-type phosphate transport system (NCBI ptt file) 103, 245
CAC1765 CAC1765 ATPase, possible competence protein ComM (NCBI ptt file) 39, 245
CAC2180 CAC2180 GDP-D-mannose dehydratase (NCBI ptt file) 177, 226
CAC2498 CAC2498 Carbon monoxide dehydrogenase, catalytic subunit (cooS) (NCBI ptt file) 177, 188
CAC2606 CAC2606 Predicted sugar-phosphate isomerase (NCBI ptt file) 177, 230
CAC2638 lonB Lon-like ATP-dependent protease (NCBI ptt file) 41, 177
CAC2815 CAC2815 Hypothetical protein (NCBI ptt file) 101, 245
CAC3009 CAC3009 Xylanase/chitin deacetylase family protein (NCBI ptt file) 177, 243
CAC3039 CAC3039 Hypothetical secreted protein (NCBI ptt file) 245, 256
CAC3166 CAC3166 Predicted DNA-binding protein (NCBI ptt file) 30, 245
CAC3421 CAC3421 Acyl carrier protein phosphodiesterase (NCBI ptt file) 177, 245
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 CAC3421
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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