Organism : Clostridium acetobutylicum | Module List :
CAC0231

Transcripcional regulator of sugar metabolism (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0231
(Mouseover regulator name to see its description)

CAC0231 is regulated by 23 influences and regulates 13 modules.
Regulators for CAC0231 (23)
Regulator Module Operator
CAC0231 12 tf
CAC0382 12 tf
CAC0393 12 tf
CAC0627 12 tf
CAC0724 12 tf
CAC1086 12 tf
CAC1455 12 tf
CAC1766 12 tf
CAC1786 12 tf
CAC2859 12 tf
CAC3214 12 tf
CAC3677 12 tf
CAC0183 204 tf
CAC0231 204 tf
CAC0254 204 tf
CAC0832 204 tf
CAC0876 204 tf
CAC1086 204 tf
CAC1333 204 tf
CAC1455 204 tf
CAC3142 204 tf
CAC3487 204 tf
CAC3649 204 tf

Warning: CAC0231 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
6678 3.50e+01 Gag.gttTG
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6679 8.50e+02 gaaA.ga.gTg
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7060 8.60e-01 aaattagaggGagg
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7061 1.50e+03 AgAagaTtTGT
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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 CAC0231

CAC0231 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators of sugar metabolism cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for CAC0231

CAC0231 has total of 26 gene neighbors in modules 12, 204
Gene neighbors (26)
Gene Common Name Description Module membership
CAC0231 CAC0231 Transcripcional regulator of sugar metabolism (NCBI ptt file) 12, 204
CAC0232 fruB 1-phosphofructokinase (fructoso 1-phosphate kinase) (NCBI ptt file) 12, 204
CAC0233 CAC0233 PTS system, IIA component (NCBI ptt file) 12, 204
CAC0234 CAC0234 PTS system, fructoso-specific IIBC component (NCBI ptt file) 12, 204
CAC1322 glpA Glycerol-3-phosphate dehydrogenase, GLPA (NCBI ptt file) 204, 327
CAC1324 CAC1324 Uncharacterized predected metal-binding protein (NCBI ptt file) 204, 363
CAC1364 CAC1364 Enzyme from phospholipase D family, possible endonuclease nuc (NCBI ptt file) 204, 366
CAC1441 CAC1441 Hypothetical protein (NCBI ptt file) 47, 204
CAC1454 CAC1454 Membrane associated histidine kinase-like ATPase (NCBI ptt file) 204, 340
CAC1455 CAC1455 Two-component system regulator (CheY domain and HTH-like DNA-binding domain) (NCBI ptt file) 204, 340
CAC1456 CAC1456 Sugar-binding periplasmic protein (NCBI ptt file) 204, 340
CAC2610 CAC2610 L-fucose isomerase related protein (NCBI ptt file) 12, 340
CAC2611 CAC2611 Hypothetical protein (NCBI ptt file) 12, 340
CAC2612 xylB Xylulose kinase (NCBI ptt file) 12, 340
CAC2703 groEL Chaperonin GroEL, HSP60 family (NCBI ptt file) 204, 271
CAC2704 groES Co-chaperonin GroES, HSP10 family (NCBI ptt file) 204, 271
CAC2810 CAC2810 Possible glucoamylase (diverged), 15 family (NCBI ptt file) 12, 204
CAC2827 CAC2827 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 80, 204
CAC2828 CAC2828 Nudix (MutT) family hydrolase/pyrophosphatase (NCBI ptt file) 80, 204
CAC3157 trpA Tryptophan synthase alpha chain (NCBI ptt file) 12, 318
CAC3158 trpB Tryptophan synthase beta chain (NCBI ptt file) 12, 318
CAC3159 trpF Phosphoribosylanthranilate isomerase (NCBI ptt file) 12, 318
CAC3160 trpC Indole-3-glycerol phosphate synthase (NCBI ptt file) 12, 318
CAC3161 trpD Anthranilate phosphoribosyltransferase (NCBI ptt file) 12, 318
CAC3162 pabA Para-aminobenzoate synthase component II (NCBI ptt file) 12, 318
CAC3163 parB Para-aminobenzoate synthase component I (NCBI ptt file) 12, 318
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 CAC0231
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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