Organism : Clostridium acetobutylicum | Module List :
CAC0978

Possible elongation subunit of DNA-dependent DNA polymerase (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted exonuclease cog/ cog
nucleic acid binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA replication go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC0978
(Mouseover regulator name to see its description)

CAC0978 is regulated by 17 influences and regulates 0 modules.
Regulators for CAC0978 (17)
Regulator Module Operator
CAC0201 5 tf
CAC0768 5 tf
CAC1578 5 tf
CAC2084 5 tf
CAC2254 5 tf
CAC3143 5 tf
CAC3152 5 tf
CAC3166 5 tf
CAC3370 5 tf
CAC0254 268 tf
CAC0255 268 tf
CAC0951 268 tf
CAC0977 268 tf
CAC1463 268 tf
CAC1668 268 tf
CAC2074 268 tf
CAC3472 268 tf

Warning: CAC0978 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
6664 2.40e-01 GGAGttGAtT
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6665 5.90e+03 CAGCGG
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7188 6.20e+00 gGGgGtaT
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7189 4.30e+02 CAActcCtAtAagtaATAgTaaAC
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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 CAC0978

CAC0978 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted exonuclease cog/ cog
nucleic acid binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA replication go/ biological_process
Module neighborhood information for CAC0978

CAC0978 has total of 40 gene neighbors in modules 5, 268
Gene neighbors (40)
Gene Common Name Description Module membership
CAC0001 dnaA DNA replication initiator protein, ATPase (NCBI ptt file) 3, 5
CAC0294 CAC0294 Magnesium and cobalt transporter (NCBI ptt file) 3, 5
CAC0504 CAC0504 FHA-domain containing secreted protein (NCBI ptt file) 58, 268
CAC0953 CAC0953 Hypothetical protein (NCBI ptt file) 25, 268
CAC0976 CAC0976 Uncharacterized conserved protein, ortholog yuzA B.subtilis (NCBI ptt file) 268, 295
CAC0977 asnC Transcriptional regulator, Lrp family (NCBI ptt file) 152, 268
CAC0978 CAC0978 Possible elongation subunit of DNA-dependent DNA polymerase (NCBI ptt file) 5, 268
CAC0988 CAC0988 Probably membrane protein (NCBI ptt file) 5, 134
CAC0996 CAC0996 Hypothetical protein (NCBI ptt file) 25, 268
CAC1102 CAC1102 Predicted membrane protein (NCBI ptt file) 25, 268
CAC1103 CAC1103 Possible metal-binding domain, related to a correspondent domain of site-specific recombinase (NCBI ptt file) 134, 268
CAC1195 ligA DNA ligase (NAD dependent), LigA (NCBI ptt file) 3, 5
CAC1214 CAC1214 Xre family DNA-binding domain and TPR-repeat containing protein (NCBI ptt file) 152, 268
CAC1245 pbpA Penicillin-binding protein 2 (NCBI ptt file) 2, 5
CAC1306 CAC1306 Hypothetical protein (NCBI ptt file) 5, 51
CAC1495 CAC1495 Enzyme of dihydrofolate reductase family, ortholog YWFD B.subtilis (NCBI ptt file) 5, 247
CAC1685 CAC1685 Uncharacterized protein from YceG family (NCBI ptt file) 5, 315
CAC1687 CAC1687 Collagenase family protease (NCBI ptt file) 5, 315
CAC1749 CAC1749 BioB/LipA-like protein (NCBI ptt file) 5, 283
CAC1793 lexA P-loop ATPase domain fused to LexA-like protein (NCBI ptt file) 3, 5
CAC1804 CAC1804 Exopolyphosphatase family protein (NCBI ptt file) 5, 213
CAC1806 CAC1806 Riboflavin kinase/FAD synthase (NCBI ptt file) 5, 213
CAC1874 CAC1874 Hypothetical protein (NCBI ptt file) 25, 268
CAC2024 CAC2024 Phosphatidylglycerophosphate synthase related protein (fragment) (NCBI ptt file) 25, 268
CAC2026 CAC2026 Predicted flavodoxin (NCBI ptt file) 25, 268
CAC2067 CAC2067 Hypothetical protein (NCBI ptt file) 51, 268
CAC2068 CAC2068 Sporulation factor spoIIM, uncharacterized membrane protein (NCBI ptt file) 51, 268
CAC2280 CAC2280 Predicted membrane protein (NCBI ptt file) 134, 268
CAC2323 CAC2323 Predicted membrane protein (NCBI ptt file) 5, 82
CAC2518 CAC2518 Extracellular neutral metalloprotease, NPRE (fragment or C-term. domain) (NCBI ptt file) 134, 268
CAC2672 CAC2672 Predicted membrane protein (NCBI ptt file) 5, 352
CAC2698 CAC2698 Hypothetical protein (NCBI ptt file) 5, 351
CAC2844 galT Galactose-1-phosphate uridylyltransferase (NCBI ptt file) 5, 100
CAC2938 CAC2938 Hypothetical protein (NCBI ptt file) 5, 62
CAC3023 CAC3023 Hypothetical protein (NCBI ptt file) 268, 292
CAC3151 rpmG L33 (NCBI ptt file) 5, 255
CAC3152 CAC3152 DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 5, 109
CAC3228 CAC3228 Predicted membrane protein (NCBI ptt file) 5, 117
CAC3417 CAC3417 Flavodoxin (NCBI ptt file) 25, 268
CAC3734 thdF Predicted GTPase, ThdF family (NCBI ptt file) 5, 100
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 CAC0978
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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