Organism : Clostridium acetobutylicum | Module List :
CAC1689 sigK

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

CircVis
Functional Annotations (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit 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
sequence-specific DNA binding go/ molecular_function
spore_sigmaK tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1689
(Mouseover regulator name to see its description)

CAC1689 is regulated by 28 influences and regulates 13 modules.
Regulators for CAC1689 sigK (28)
Regulator Module Operator
CAC0113 315 tf
CAC0197 315 tf
CAC0382 315 tf
CAC0856 315 tf
CAC1467 315 tf
CAC1689 315 tf
CAC1696 315 tf
CAC1753 315 tf
CAC1799 315 tf
CAC2084 315 tf
CAC2143 315 tf
CAC2259 315 tf
CAC2473 315 tf
CAC2546 315 tf
CAC2773 315 tf
CAC2950 315 tf
CAC3166 315 tf
CAC3192 315 tf
CAC3418 315 tf
CAC3502 315 tf
CAC0863 39 tf
CAC1430 39 tf
CAC1469 39 tf
CAC1689 39 tf
CAC2616 39 tf
CAC2794 39 tf
CAC2859 39 tf
CAC3729 39 tf

Warning: CAC1689 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
6732 4.30e+04 GTGTGG
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6733 3.60e-03 aaaGGAGG
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7282 4.10e-01 gGAGttGg
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7283 7.50e+01 ctGtAGcaAg
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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 CAC1689

CAC1689 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA-directed RNA polymerase specialized sigma subunit 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
sequence-specific DNA binding go/ molecular_function
spore_sigmaK tigr/ tigrfam
Module neighborhood information for CAC1689

CAC1689 has total of 47 gene neighbors in modules 39, 315
Gene neighbors (47)
Gene Common Name Description Module membership
CAC0300 CAC0300 DNA-polymerase III, gamma subunit (NCBI ptt file) 315, 329
CAC0344 CAC0344 Hypothetical protein (NCBI ptt file) 39, 95
CAC0470 spmB Spore maturation protein B (gene spmB) (NCBI ptt file) 15, 39
CAC0491 CAC0491 Uncharacterized probably secreted protein, homolog of YDCC B.subtilis (NCBI ptt file) 56, 315
CAC0779 CAC0779 Amidase related to nicotinamidase (NCBI ptt file) 39, 62
CAC0863 CAC0863 Sensory transduction histidine kinase (NCBI ptt file) 39, 300
CAC1026 CAC1026 Superfamily I DNA helicase (NCBI ptt file) 213, 315
CAC1093 CAC1093 Hypothetical secreted protein (NCBI ptt file) 39, 330
CAC1243 mreC Shape-determining protein mreC (NCBI ptt file) 2, 315
CAC1270 CAC1270 Hypothetical protein (NCBI ptt file) 39, 203
CAC1276 SpoIIP Stage II sporulation protein P (NCBI ptt file) 39, 330
CAC1305 CAC1305 Uncharacterized protein similar to a protein from Cylindrotheca fusiformis plasmid (GI:99322) (NCBI ptt file) 51, 315
CAC1326 CAC1326 Uncharacterized protein homolog T.maritima (4980675) (NCBI ptt file) 39, 95
CAC1402 CAC1402 Unchracterized conserved protein, similar to IcaC of Staphylococcus; YHJR B.subtilis family (NCBI ptt file) 39, 95
CAC1403 CAC1403 Zn-dependent hydrolase, glyoxylase II family (NCBI ptt file) 100, 315
CAC1466 CAC1466 Hypothetical protein (NCBI ptt file) 39, 236
CAC1468 CAC1468 Predicted acetyltransferase (NCBI ptt file) 174, 315
CAC1473 CAC1473 Proline/glycine betaine ABC-type transport system, permease component (NCBI ptt file) 39, 177
CAC1508 CAC1508 Hypothetical protein (NCBI ptt file) 39, 300
CAC1684 CAC1684 TYPA/BIPA type GTPase (NCBI ptt file) 142, 315
CAC1685 CAC1685 Uncharacterized protein from YceG family (NCBI ptt file) 5, 315
CAC1686 CAC1686 S-adenosylmethionine-dependent methyltransferase (NCBI ptt file) 315, 329
CAC1687 CAC1687 Collagenase family protease (NCBI ptt file) 5, 315
CAC1689 sigK DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) 39, 315
CAC1725 CAC1725 Predicted rRNA methylase, SUN family (NCBI ptt file) 159, 315
CAC1729 CAC1729 Predicted GTPase (YLOQ B.subtilis ortholog) (NCBI ptt file) 213, 315
CAC1730 CAC1730 Pentose-5-phosphate-3-epimerase, YLOR B.subtilis ortholog (NCBI ptt file) 315, 329
CAC1765 CAC1765 ATPase, possible competence protein ComM (NCBI ptt file) 39, 245
CAC1784 smf DNA uptake protein (NCBI ptt file) 39, 102
CAC1790 frr Ribosome recycling factor (NCBI ptt file) 310, 315
CAC1823 CAC1823 Uncharacterized conserved protein (NCBI ptt file) 51, 315
CAC1824 clpA ATP-dependent Clp proteinase (NCBI ptt file) 51, 315
CAC1829 CAC1829 Predicted inactivated Zn-dependent peptidase, PMBA ortholog (NCBI ptt file) 312, 315
CAC1839 CAC1839 Hypothetical protein (NCBI ptt file) 39, 300
CAC2058 CAC2058 Predicted membrane protein (NCBI ptt file) 39, 330
CAC2232 recJ SsDNA Exonuclease, RecJ (NCBI ptt file) 22, 315
CAC2300 CAC2300 Uncharacterized secreted protein, YunB B.subtilis homolog (NCBI ptt file) 39, 300
CAC2582 CAC2582 Uncharacterized conserved membrane protein, YHGE B.subtilis homolog (NCBI ptt file) 39, 300
CAC2673 CAC2673 NAD-dependent DNA ligase (NCBI ptt file) 35, 315
CAC2790 CAC2790 Hypothetical protein (NCBI ptt file) 39, 300
CAC2843 CAC2843 Protein containing aminopeptidase domain (iap family) (NCBI ptt file) 39, 279
CAC2874 CAC2874 UDP-N-acetylglucosamine 2-epimerase (NCBI ptt file) 137, 315
CAC2899 CAC2899 LysM repeats domain containing membrane protein (NCBI ptt file) 39, 330
CAC3015 CAC3015 Glycosyltransferase (NCBI ptt file) 39, 300
CAC3032 CAC3032 Galactose mutarotase related enzyme (NCBI ptt file) 174, 315
CAC3080 CAC3080 Hypothetical protein (NCBI ptt file) 39, 41
CAC3594 CAC3594 Glycosyltransferase (NCBI ptt file) 142, 315
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 CAC1689
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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