Organism : Clostridium acetobutylicum | Module List :
CAC1946

Phage related transcriptional regulator (Xre family) (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for CAC1946
(Mouseover regulator name to see its description)

CAC1946 is regulated by 13 influences and regulates 9 modules.
Regulators for CAC1946 (13)
Regulator Module Operator
CAC0681 332 tf
CAC1578 332 tf
CAC1867 332 tf
CAC1900 332 tf
CAC1946 332 tf
CAC2306 332 tf
CAC2307 332 tf
CAC3192 332 tf
CAC1867 121 tf
CAC1900 121 tf
CAC1946 121 tf
CAC1950 121 tf
CAC2966 121 tf

Warning: CAC1946 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
6894 7.20e+01 T.GGgtg
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6895 3.50e+03 gA.atatg.cg.A.Ac.T
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7316 1.30e+01 GGaGGA
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7317 4.90e+02 TtgcatTca.AagTcaAc.TTtT
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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 CAC1946

CAC1946 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for CAC1946

CAC1946 has total of 45 gene neighbors in modules 121, 332
Gene neighbors (45)
Gene Common Name Description Module membership
CAC0249 CAC0249 Glyoxalase I (glyoxalase family) (NCBI ptt file) 102, 332
CAC0382 levR Possible transcriptional regulator of levanase operon, AAA-ATPase domain (NtrC family), fused to 2 BglG-like domains, ortholog of B.subtilis levR (NCBI ptt file) 324, 332
CAC0743 CAC0743 6-phospho-beta-glucosidase (NCBI ptt file) 172, 332
CAC1660 CAC1660 Butyrate kinase, buk (NCBI ptt file) 332, 359
CAC1676 CAC1676 Uncharacterized conserved protein (NCBI ptt file) 301, 332
CAC1871 CAC1871 FtsK-like DNA segregation ATPase, YDCQ B.subtilis ortholog (NCBI ptt file) 332, 342
CAC1875 CAC1875 Hypothetical protein, CF-36 family (NCBI ptt file) 121, 180
CAC1876 lyc N-acetylmuramidase, autolytic enzyme, family 25 of glycosyl hydrolases ; peptodoglycan-binding domain (NCBI ptt file) 121, 180
CAC1877 CAC1877 Hypothetical protein, CF-8 family (NCBI ptt file) 121, 180
CAC1878 CAC1878 Hypothetical protein (NCBI ptt file) 121, 180
CAC1879 CAC1879 Uncharacterized, phage-related protein (NCBI ptt file) 121, 180
CAC1880 CAC1880 Hypothetical protein, CF-35 family (NCBI ptt file) 121, 180
CAC1881 CAC1881 Hypothetical protein (NCBI ptt file) 121, 332
CAC1882 CAC1882 Hypothetical protein (NCBI ptt file) 121, 180
CAC1883 CAC1883 Uncharacterized phage related protein (NCBI ptt file) 121, 180
CAC1884 CAC1884 Hypothetical protein (NCBI ptt file) 121, 180
CAC1885 CAC1885 Hypothetical protein (NCBI ptt file) 121, 180
CAC1886 CAC1886 Uncharacterized phage related protein (NCBI ptt file) 121, 180
CAC1887 CAC1887 Hypothetical protein (NCBI ptt file) 121, 180
CAC1888 CAC1888 Uncharacterized phage related protein (NCBI ptt file) 121, 180
CAC1889 CAC1889 Uncharacterized phage related protein (NCBI ptt file) 121, 180
CAC1890 CAC1890 Phage related protein, possible DNA packing (NCBI ptt file) 121, 180
CAC1892 CAC1892 Hypothetical protein (NCBI ptt file) 180, 332
CAC1893 CAC1893 ClpP family serine protease, possible phage related (NCBI ptt file) 180, 332
CAC1894 CAC1894 Phage-related, head portal protein (NCBI ptt file) 180, 332
CAC1895 CAC1895 Phage terminase-like protein, large subunit (NCBI ptt file) 54, 332
CAC1896 CAC1896 Phage terminase-like protein, small subunit (NCBI ptt file) 121, 180
CAC1897 CAC1897 Phage-related, Zn finger domain containing protein (NCBI ptt file) 121, 180
CAC1898 CAC1898 Hypothetical protein (NCBI ptt file) 121, 180
CAC1899 CAC1899 Hypothetical protein (NCBI ptt file) 121, 180
CAC1902 CAC1902 Hypothetical protein (NCBI ptt file) 121, 180
CAC1903 CAC1903 Hypothetical protein (NCBI ptt file) 121, 180
CAC1904 CAC1904 Hypothetical protein (NCBI ptt file) 121, 180
CAC1905 CAC1905 Hypothetical protein (NCBI ptt file) 121, 171
CAC1906 CAC1906 Hypothetical protein (NCBI ptt file) 121, 180
CAC1907 CAC1907 Hypothetical protein (NCBI ptt file) 121, 180
CAC1908 CAC1908 Predicted membrane protein (NCBI ptt file) 121, 180
CAC1912 CAC1912 Uncharacterized phage related protein (NCBI ptt file) 121, 366
CAC1913 CAC1913 Zn-finger containing protein (NCBI ptt file) 121, 180
CAC1916 CAC1916 Hypothetical protein (NCBI ptt file) 54, 332
CAC1918 CAC1918 Hypothetical protein (NCBI ptt file) 54, 332
CAC1944 CAC1944 Hypothetical protein (NCBI ptt file) 54, 332
CAC1946 CAC1946 Phage related transcriptional regulator (Xre family) (NCBI ptt file) 121, 332
CAC1951 CAC1951 Site-specific recombinases, DNA invertase Pin homolog (NCBI ptt file) 44, 332
CAC2669 CAC2669 Glu-tRNAGln amidotransferase subunit B (NCBI ptt file) 79, 332
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 CAC1946
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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