Organism : Clostridium acetobutylicum | Module List :
CAC3152

DNA-dependent RNA polymerase sigma subunit (NCBI ptt file)

CircVis
Functional Annotations (12)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
spore_sigH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC3152
(Mouseover regulator name to see its description)

CAC3152 is regulated by 19 influences and regulates 11 modules.
Regulators for CAC3152 (19)
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
CAC0113 109 tf
CAC0254 109 tf
CAC1696 109 tf
CAC1928 109 tf
CAC2060 109 tf
CAC2297 109 tf
CAC3152 109 tf
CAC3166 109 tf
CAC3247 109 tf
CAC3418 109 tf

Warning: CAC3152 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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6870 8.10e-02 CaCCTct
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6871 2.50e+03 GGaGTG
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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 CAC3152

CAC3152 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
spore_sigH tigr/ tigrfam
Module neighborhood information for CAC3152

CAC3152 has total of 49 gene neighbors in modules 5, 109
Gene neighbors (49)
Gene Common Name Description Module membership
CAC0001 dnaA DNA replication initiator protein, ATPase (NCBI ptt file) 3, 5
CAC0089 serA D-3 phosphoglycerate dehydrogenase (NCBI ptt file) 109, 343
CAC0090 CAC0090 Xylanase/chitin deacetylase, NodB family (NCBI ptt file) 109, 312
CAC0225 CAC0225 Sensory transduction histidine kinase (NCBI ptt file) 57, 109
CAC0277 CAC0277 HD-GYP hydrolase domain containing protein (NCBI ptt file) 109, 298
CAC0294 CAC0294 Magnesium and cobalt transporter (NCBI ptt file) 3, 5
CAC0452 CAC0452 Permease (NCBI ptt file) 99, 109
CAC0641 CAC0641 Uncharacterized conserved protein (NCBI ptt file) 109, 348
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
CAC1098 polA DNA polymerase I, polA (NCBI ptt file) 99, 109
CAC1195 ligA DNA ligase (NAD dependent), LigA (NCBI ptt file) 3, 5
CAC1245 pbpA Penicillin-binding protein 2 (NCBI ptt file) 2, 5
CAC1297 CAC1297 N-terminal fragment of elongation factor Ts (NCBI ptt file) 49, 109
CAC1306 CAC1306 Hypothetical protein (NCBI ptt file) 5, 51
CAC1312 CAC1312 Hypothetical protein (NCBI ptt file) 109, 176
CAC1404 CAC1404 Transcriptional regulator of sugar metabolism (deoR family) (NCBI ptt file) 64, 109
CAC1495 CAC1495 Enzyme of dihydrofolate reductase family, ortholog YWFD B.subtilis (NCBI ptt file) 5, 247
CAC1539 CAC1539 Gamma-glutamylcysteine synthetase (NCBI ptt file) 109, 222
CAC1559 CAC1559 Predicted transcriptional regulator (NCBI ptt file) 109, 151
CAC1635 CAC1635 Predicted nucleic acid binding protein, containing 2 S1 domains, YITL B.subtilis ortholog (NCBI ptt file) 109, 312
CAC1651 CAC1651 Predicted GTPase with uncharacterized domain, ortholog of T.maritima (4980952) (NCBI ptt file) 109, 283
CAC1652 aspA Aspartate ammonia-lyase (NCBI ptt file) 109, 329
CAC1661 CAC1661 Predicted secreted nucleic acid binding protein (NCBI ptt file) 25, 109
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
CAC1955 CAC1955 Hypothetical protein (NCBI ptt file) 57, 109
CAC1965 greA Transcription elongation factor GreA (NCBI ptt file) 63, 109
CAC2037 CAC2037 Hypothetical protein, CF-39 family (NCBI ptt file) 109, 312
CAC2323 CAC2323 Predicted membrane protein (NCBI ptt file) 5, 82
CAC2437 CAC2437 Uncharacterized conserved protein (NCBI ptt file) 100, 109
CAC2672 CAC2672 Predicted membrane protein (NCBI ptt file) 5, 352
CAC2698 CAC2698 Hypothetical protein (NCBI ptt file) 5, 351
CAC2787 CAC2787 Serine/threonine protein phosphatase (NCBI ptt file) 109, 128
CAC2844 galT Galactose-1-phosphate uridylyltransferase (NCBI ptt file) 5, 100
CAC2873 CAC2873 Acetyl-CoA acetyltransferase (NCBI ptt file) 10, 109
CAC2938 CAC2938 Hypothetical protein (NCBI ptt file) 5, 62
CAC3151 rpmG L33 (NCBI ptt file) 5, 255
CAC3152 CAC3152 DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 5, 109
CAC3155 CAC3155 Uncharacterized conserved protein, THY1 family (NCBI ptt file) 19, 109
CAC3221 prs Phosphoribosylpyrophosphate synthetase (NCBI ptt file) 109, 251
CAC3228 CAC3228 Predicted membrane protein (NCBI ptt file) 5, 117
CAC3307 CAC3307 TPR-repeats containing protein (NCBI ptt file) 109, 190
CAC3602 CAC3602 HD superfamily hydrolase (NCBI ptt file) 86, 109
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 CAC3152
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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