Organism : Clostridium acetobutylicum | Module List :
CAC2711 bcd

Butyryl-CoA dehydrogenase (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Acyl-CoA dehydrogenases cog/ cog
acyl-CoA dehydrogenase activity go/ molecular_function
electron transport go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC2711
(Mouseover regulator name to see its description)

CAC2711 is regulated by 16 influences and regulates 0 modules.
Regulators for CAC2711 bcd (16)
Regulator Module Operator
CAC0707 255 tf
CAC1799 255 tf
CAC2259 255 tf
CAC2552 255 tf
CAC3104 255 tf
CAC3142 255 tf
CAC3143 255 tf
CAC3149 255 tf
CAC3271 255 tf
CAC3677 255 tf
CAC0115 232 tf
CAC0493 232 tf
CAC2222 232 tf
CAC3037 232 tf
CAC3579 232 tf
CAC3647 232 tf

Warning: CAC2711 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
7116 7.50e-02 agGaGgtggag
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7117 1.90e+03 GCCCGT
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7162 5.50e-01 gGAc.tG
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7163 4.30e+02 AgGagGataat
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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 CAC2711

CAC2711 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Acyl-CoA dehydrogenases cog/ cog
acyl-CoA dehydrogenase activity go/ molecular_function
electron transport go/ biological_process
flavin adenine dinucleotide binding go/ molecular_function
Module neighborhood information for CAC2711

CAC2711 has total of 39 gene neighbors in modules 232, 255
Gene neighbors (39)
Gene Common Name Description Module membership
CAC0115 CAC0115 Uncharacterized protein, Yje/RRF2 family (NCBI ptt file) 63, 232
CAC0322 CAC0322 Sensory protein, containing EAL-domain (NCBI ptt file) 232, 295
CAC0493 CAC0493 Uncharcterized small conserved protein, YhhG family (NCBI ptt file) 64, 232
CAC0494 CAC0494 PemK family of DNA-binding proteins (NCBI ptt file) 32, 232
CAC0748 CAC0748 Nitroreductase family protein (NCBI ptt file) 154, 255
CAC1242 mreB mreB (NCBI ptt file) 35, 255
CAC1289 CAC1289 Uncharacterized conserved protein, YqeY B.subtilis ortholog (NCBI ptt file) 32, 232
CAC1745 rpmF Ribosomal protein L32 (NCBI ptt file) 32, 232
CAC1747 acpA Acyl carrier protein, ACP (NCBI ptt file) 32, 232
CAC2710 etfB Electron transfer flavoprotein beta-subunit (NCBI ptt file) 255, 259
CAC2711 bcd Butyryl-CoA dehydrogenase (NCBI ptt file) 232, 255
CAC2712 crt Crotonase (3-hydroxybutyryl-COA dehydratase) (NCBI ptt file) 61, 232
CAC2856 metK S-adenosylmethionine synthetase (NCBI ptt file) 32, 232
CAC3004 folA Dihydrofolate reductase (NCBI ptt file) 255, 258
CAC3087 CAC3087 Phosphoenolpyruvate-protein kinase (PTS system enzyme I) (NCBI ptt file) 4, 255
CAC3099 truA Pseudouridylate synthase, TRUA (NCBI ptt file) 106, 255
CAC3101 CAC3101 ABC-type transporter, ATPase component (cobalt transporters subfamily) (NCBI ptt file) 79, 255
CAC3102 CAC3102 ABC-type transporter, ATPase component (cobalt transporters subfamily) (NCBI ptt file) 255, 358
CAC3107 rpsM Ribosomal protein S13 (NCBI ptt file) 255, 358
CAC3109 infA Translation initiation factor IF-1 (NCBI ptt file) 255, 292
CAC3110 CAC3110 Ribosomal protein L14E (archaeal/eukaryotic type) (NCBI ptt file) 255, 358
CAC3118 rplF Ribosomal protein L6 (NCBI ptt file) 255, 358
CAC3122 rplX Ribosomal protein L24 (NCBI ptt file) 255, 304
CAC3125 rpmC Ribosomal protein L29 (NCBI ptt file) 255, 358
CAC3129 rpsS Ribosomal protein S19 (NCBI ptt file) 237, 255
CAC3131 rplW Ribosomal protein L23 (NCBI ptt file) 116, 255
CAC3133 rplC Ribosomal protein L3 (NCBI ptt file) 254, 255
CAC3135 CAC3135 Uncharacterized C4-type Zn-finger containing protein (NCBI ptt file) 232, 237
CAC3142 rpoC DNA-dependent RNA polymerase beta' subunit (NCBI ptt file) 255, 335
CAC3143 rpoB DNA-dependent RNA polymerase beta subunit (NCBI ptt file) 255, 335
CAC3145 rplL Ribosomal protein L7/L12 (NCBI ptt file) 61, 232
CAC3147 rplA Ribosomal protein L1 (NCBI ptt file) 61, 232
CAC3149 nusG Transcription antiterminator NusG (NCBI ptt file) 116, 255
CAC3150 secE Preprotein translocase subunit SecE (NCBI ptt file) 116, 232
CAC3151 rpmG L33 (NCBI ptt file) 5, 255
CAC3222 gcaD UDP-N-acetylglucosamine pyrophosphorylase (NCBI ptt file) 255, 312
CAC3224 purR PUR operon repressor, Adenine/guanine phosphoribosyltransferase family (NCBI ptt file) 232, 292
CAC3252 proC Pyrroline-5-carboxylate reductase (NCBI ptt file) 85, 232
CAC3394 CAC3394 Uncharacterized conserved protein, YGIN family (NCBI ptt file) 232, 292
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 CAC2711
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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