Organism : Clostridium acetobutylicum | Module List :
CAC1223 dnaE

DNA Polymerase III Alpha chain (dnaE) (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
DNA polymerase III, alpha subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
cytoplasm go/ cellular_component
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
polc tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1223
(Mouseover regulator name to see its description)

CAC1223 is regulated by 13 influences and regulates 0 modules.
Regulators for CAC1223 dnaE (13)
Regulator Module Operator
CAC0254 101 tf
CAC0255 101 tf
CAC1698 101 tf
CAC1915 101 tf
CAC1928 101 tf
CAC1941 101 tf
CAC3475 101 tf
CAC0115 187 tf
CAC0693 187 tf
CAC1226 187 tf
CAC1867 187 tf
CAC2473 187 tf
CAC3438 187 tf

Warning: CAC1223 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
6854 3.40e-02 aGgaGGtaata
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6855 3.10e+03 GgaGaAgtCa.AgaacCaggTcA
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7026 3.60e-03 gAaGGaGG
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7027 1.70e+02 TAAttggtgGaG
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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 CAC1223

CAC1223 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA polymerase III, alpha subunit cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
cytoplasm go/ cellular_component
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
polc tigr/ tigrfam
Module neighborhood information for CAC1223

CAC1223 has total of 37 gene neighbors in modules 101, 187
Gene neighbors (37)
Gene Common Name Description Module membership
CAC0564 CAC0564 Response regulator (REC, HTH domains) (NCBI ptt file) 101, 347
CAC0565 CAC0565 Histidine kinase (HAMP, HisKA and HATPase domains) (NCBI ptt file) 101, 347
CAC0740 CAC0740 Uncharacterized conserved protein, YlxP family (NCBI ptt file) 101, 210
CAC1114 CAC1114 Hypothetical protein (NCBI ptt file) 187, 195
CAC1115 CAC1115 Hypothetical protein (NCBI ptt file) 187, 195
CAC1118 CAC1118 Phage related protein (NCBI ptt file) 104, 187
CAC1119 CAC1119 Hypothetical protein (NCBI ptt file) 187, 253
CAC1133 CAC1133 Phage related protein, YonE B.subtilis homolog (NCBI ptt file) 187, 195
CAC1158 CAC1158 Hypothetical protein (NCBI ptt file) 187, 361
CAC1161 CAC1161 Predicted ATPase of HSP70 class (NCBI ptt file) 187, 326
CAC1164 CAC1164 Hypothetical protein (NCBI ptt file) 101, 104
CAC1168 CAC1168 Uncharacterized conserved protein (NCBI ptt file) 187, 361
CAC1177 CAC1177 Hypothetical protein (NCBI ptt file) 187, 275
CAC1179 CAC1179 Hypothetical protein (NCBI ptt file) 173, 187
CAC1181 CAC1181 Phage related protein, YorF B.subtilis homolog (NCBI ptt file) 16, 187
CAC1188 CAC1188 Hypothetical protein (NCBI ptt file) 187, 246
CAC1190 CAC1190 Predicted Fe-S-cluster redox enzyme, YLON B.subtilis homolog (NCBI ptt file) 187, 253
CAC1192 CAC1192 Phage replicative DNA helicase, YorI B.subtilis homolog (NCBI ptt file) 187, 253
CAC1198 recJ Single-stranded-DNA-specific exonuclease (recJ) (NCBI ptt file) 187, 326
CAC1200 CAC1200 Similar to phospho-adenylylsulfate sulfotransferase (NCBI ptt file) 104, 187
CAC1208 CAC1208 Hypothetical protein (NCBI ptt file) 187, 338
CAC1209 nrdD Anaerobic ribonucleotide reductase (NCBI ptt file) 187, 253
CAC1211 CAC1211 Hypothetical protein (NCBI ptt file) 187, 275
CAC1212 CAC1212 Hypothetical protein (NCBI ptt file) 187, 275
CAC1222 CAC1222 DNA-methyltransferase (cytosine-specific) (NCBI ptt file) 101, 161
CAC1223 dnaE DNA Polymerase III Alpha chain (dnaE) (NCBI ptt file) 101, 187
CAC1535 CAC1535 ABC transporter, ATPase component (NCBI ptt file) 101, 347
CAC1919 CAC1919 Phage related SSB-like protein (NCBI ptt file) 101, 175
CAC1924 CAC1924 Hypothetical protein (NCBI ptt file) 101, 175
CAC1927 CAC1927 Hypothetical protein, CF-31 family (NCBI ptt file) 101, 175
CAC1929 CAC1929 Hypothetical protein (NCBI ptt file) 101, 175
CAC1936 CAC1936 Hypothetical protein (NCBI ptt file) 101, 175
CAC2741 gpmA Phosphoglycerate mutase (NCBI ptt file) 78, 101
CAC2815 CAC2815 Hypothetical protein (NCBI ptt file) 101, 245
CAC3514 CAC3514 Reverse transcriptase/maturase family protein (NCBI ptt file) 101, 347
CAC3521 CAC3521 Hypothetical protein (NCBI ptt file) 101, 347
CAC3698 CAC3698 Hypothetical protein, CF-44 family (NCBI ptt file) 101, 347
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 CAC1223
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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