Organism : Clostridium acetobutylicum | Module List :
CAC3166

Predicted DNA-binding protein (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Predicted DNA-binding proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3166
(Mouseover regulator name to see its description)

CAC3166 is regulated by 18 influences and regulates 21 modules.
Regulators for CAC3166 (18)
Regulator Module Operator
CAC0240 30 tf
CAC0254 30 tf
CAC0474 30 tf
CAC0599 30 tf
CAC1578 30 tf
CAC1682 30 tf
CAC2471 30 tf
CAC2486 30 tf
CAC2818 30 tf
CAC3166 30 tf
CAC3224 30 tf
CAC3418 30 tf
CAC0255 245 tf
CAC1766 245 tf
CAC2471 245 tf
CAC2793 245 tf
CAC3166 245 tf
CAC3603 245 tf

Warning: CAC3166 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
6714 2.10e-01 gGtGagG
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6715 6.60e+02 GAGccCTGGAAGcTG
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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 CAC3166

CAC3166 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Predicted DNA-binding proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Module neighborhood information for CAC3166

CAC3166 has total of 35 gene neighbors in modules 30, 245
Gene neighbors (35)
Gene Common Name Description Module membership
CAC0123 CAC0123 Cytosine deaminase (NCBI ptt file) 30, 223
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
CAC0545 CAC0545 Uncharacterized small protein, homolog of Treponema (6136517) (NCBI ptt file) 30, 210
CAC0643 CAC0643 Putative spore germination protein (NCBI ptt file) 136, 245
CAC0770 CAC0770 Glycerol uptake facilitator protein, permease (NCBI ptt file) 30, 316
CAC1066 CAC1066 Hypothetical protein (NCBI ptt file) 30, 327
CAC1082 CAC1082 Hypothetical protein (NCBI ptt file) 30, 327
CAC1095 CAC1095 Uncharacterized protein, YjiN homolog (NCBI ptt file) 30, 230
CAC1137 CAC1137 Hypothetical protein (NCBI ptt file) 30, 272
CAC1201 CAC1201 Hypothetical protein (NCBI ptt file) 30, 104
CAC1216 CAC1216 Hypothetical protein (NCBI ptt file) 30, 173
CAC1268 comEA Competence ComEA protein (NCBI ptt file) 243, 245
CAC1269 CAC1269 Cation transport ATPase (NCBI ptt file) 30, 105
CAC1421 CAC1421 Pyruvate-formate lyase-activating enzyme (NCBI ptt file) 188, 245
CAC1505 CAC1505 Hypothetical protein (NCBI ptt file) 245, 257
CAC1547 trxA Thioredoxin, trx (NCBI ptt file) 30, 220
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
CAC2421 CAC2421 Predicted enzyme with TIM-barrel fold (NCBI ptt file) 30, 327
CAC2651 pyrZ Dihydroorotate dehydrogenase electron transfer subunit (NCBI ptt file) 30, 116
CAC2739 CAC2739 Predicted acetyltransferase (NCBI ptt file) 30, 47
CAC2815 CAC2815 Hypothetical protein (NCBI ptt file) 101, 245
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
CAC3446 CAC3446 Predicted epimerase, PhzC/PhzF homolog (NCBI ptt file) 30, 220
CAC3458 CAC3458 Uncharacterized protein, homolog of B. anthracis (gi:48942631) (NCBI ptt file) 30, 220
CAC3623 CAC3623 Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) (NCBI ptt file) 4, 30
CAC3627 CAC3627 PP-loop superfamily ATPase, confers aluminum resistance (NCBI ptt file) 30, 193
CAC3725 CAC3725 Uncharacterized protein, homolog of Streptococcus pneumoniae (gi:2109447) (NCBI ptt file) 30, 120
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 CAC3166
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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