Organism : Clostridium acetobutylicum | Module List :
CAC3715 dnaC

Replicative DNA helicase, DNAC (NCBI ptt file)

CircVis
Functional Annotations (8)
Function System
Replicative DNA helicase cog/ cog
DNA binding go/ molecular_function
DNA helicase activity go/ molecular_function
ATP binding go/ molecular_function
DNA replication go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
DnaB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3715
(Mouseover regulator name to see its description)

CAC3715 is regulated by 21 influences and regulates 0 modules.
Regulators for CAC3715 dnaC (21)
Regulator Module Operator
CAC0162 335 tf
CAC0707 335 tf
CAC0863 335 tf
CAC0933 335 tf
CAC1032 335 tf
CAC1300 335 tf
CAC1320 335 tf
CAC1832 335 tf
CAC2430 335 tf
CAC3142 335 tf
CAC3149 335 tf
CAC3199 335 tf
CAC0144 243 tf
CAC0284 243 tf
CAC0474 243 tf
CAC0863 243 tf
CAC0865 243 tf
CAC1469 243 tf
CAC1698 243 tf
CAC3472 243 tf
CAC3475 243 tf

Warning: CAC3715 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
7138 2.40e+02 CA.tC.ACC
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7139 2.60e+02 aAGgAGg
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7322 1.20e-05 gGAGAGGatG
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7323 9.80e+02 GCCTTCACcCC
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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 CAC3715

CAC3715 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Replicative DNA helicase cog/ cog
DNA binding go/ molecular_function
DNA helicase activity go/ molecular_function
ATP binding go/ molecular_function
DNA replication go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
DnaB tigr/ tigrfam
Module neighborhood information for CAC3715

CAC3715 has total of 37 gene neighbors in modules 243, 335
Gene neighbors (37)
Gene Common Name Description Module membership
CAC0088 CAC0088 Peptide methionine sulfoxide reductase (NCBI ptt file) 243, 343
CAC0298 CAC0298 Guanylate kinase (NCBI ptt file) 226, 243
CAC0502 uvrB Excinuclease ABC subunit B (helicase subunit of the DNA excision repair complex) (NCBI ptt file) 154, 335
CAC0503 uvrA Excinuclease ABC subunit A (ATP-ase), (uvrA) (NCBI ptt file) 154, 335
CAC0620 CAC0620 ABC transporter, periplasmic-binding, putative (NCBI ptt file) 181, 243
CAC0710 pgk 3-phosphoglycerate kinase (NCBI ptt file) 79, 335
CAC1268 comEA Competence ComEA protein (NCBI ptt file) 243, 245
CAC1735 CAC1735 Predicted kinase related to hydroxyacetone kinase, YLOV ortholog (NCBI ptt file) 36, 335
CAC1743 askA Acetate kinase (NCBI ptt file) 335, 343
CAC1748 rncS DsRNA-specific ribonuclease III (NCBI ptt file) 271, 335
CAC1975 CAC1975 Hypothetical secreted protein (NCBI ptt file) 226, 243
CAC2035 CAC2035 Hypothetical protein, CF-23 family (NCBI ptt file) 226, 243
CAC2411 CAC2411 Zn-dependent protease of MPP family (NCBI ptt file) 105, 335
CAC2435 CAC2435 Response regulator (CheY-like domain and HTH-type DNA-binding domain) (NCBI ptt file) 243, 271
CAC2447 CAC2447 Hypothetical protein (NCBI ptt file) 226, 243
CAC2799 CAC2799 Uncharacterized conserved protein, similar to lppY/lpqO of M.tuberculosis (NCBI ptt file) 181, 243
CAC2845 prfB Protein chain release factor B (NCBI ptt file) 329, 335
CAC2864 atpC FoF1-type ATP synthase epsilon subunit (NCBI ptt file) 304, 335
CAC2866 atpG FoF1-type ATP synthase gamma subunit (NCBI ptt file) 59, 335
CAC2867 atpA FoF1-type ATP synthase alpha subunit (NCBI ptt file) 59, 335
CAC2868 atpH FoF1-type ATP synthase delta subunit (NCBI ptt file) 59, 335
CAC2869 atpF FoF1-type ATP synthase B subunit (NCBI ptt file) 79, 335
CAC3006 CAC3006 Zn-dependent peptidase, insulinase family (NCBI ptt file) 243, 329
CAC3009 CAC3009 Xylanase/chitin deacetylase family protein (NCBI ptt file) 177, 243
CAC3017 CAC3017 Predicted xylanase/chitin deacetylase (NCBI ptt file) 36, 335
CAC3079 CAC3079 Uncharacterized conserved protein, YPPB B.subtilis ortholog (NCBI ptt file) 226, 243
CAC3112 adk Adenylate kinase (NCBI ptt file) 335, 362
CAC3114 rplO Ribosomal protein L15 (NCBI ptt file) 59, 335
CAC3120 rpsN Ribosomal protein S14 (NCBI ptt file) 335, 362
CAC3136 tufA Elongation Factor Tu (Ef-Tu) (NCBI ptt file) 78, 335
CAC3138 fus Translation elongation factor EF-G (NCBI ptt file) 36, 335
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
CAC3563 CAC3563 Mismatch repair protein MutS-like ATPase (NCBI ptt file) 247, 335
CAC3574 fabG 3-ketoacyl-acyl carrier protein reductase (NCBI ptt file) 243, 337
CAC3715 dnaC Replicative DNA helicase, DNAC (NCBI ptt file) 243, 335
CAC3717 rplI Ribosomal protein L9 (NCBI ptt file) 114, 243
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 CAC3715
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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