Organism : Clostridium acetobutylicum | Module List:
Module 64 Profile

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
Network Help

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges.

Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif
Regulators for Module 64

There are 9 regulatory influences for Module 64

Regulator Table (9)
Regulator Name Type
CAC0514 tf
CAC0493 tf
CAC2934 tf
CAC3166 tf
CAC1404 tf
CAC2052 tf
CAC2473 tf
CAC0929 tf
CAC2851 tf

Regulator Help

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type.

tf: Transcription factor

ef: Environmental factor

combiner: Combinatorial influence of a tf or an ef through logic gate. Table is sortable by clicking on the arrows next to column headers.

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
6782 2.30e-03 AGGaGG
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6783 1.20e+04 GCaGcCc
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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

Regulon 64 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Unknown function tigr mainrole 5.47e-03 7.74e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 2.04e-03 3.84e-03 10/30
Transcription cog subcategory 3.14e-03 5.79e-03 6/30
Functions Help

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

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.

Members for Module 64

There are 30 genes in Module 64

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0005 CAC0005 CDS None chromosome 4489 4821 + Uncharacterized small conserved protein, ortholog of YAAB B.subtilis (NCBI ptt file) False
CAC0006 gyrB CDS None chromosome 4844 6757 + DNA gyrase (topoisomerase II) B subunit (NCBI ptt file) False
CAC0296 csfB CDS None chromosome 352628 352843 + Zn-finger containing protein, csfB B.subtilis homolog (NCBI ptt file) False
CAC0493 CAC0493 CDS None chromosome 567127 567447 + Uncharcterized small conserved protein, YhhG family (NCBI ptt file) True
CAC0514 CAC0514 CDS None chromosome 590854 592158 + CBS domain, similar to B.subtilis ytoI (NCBI ptt file) True
CAC0531 CAC0531 CDS None chromosome 614278 615051 + Transcriptional regulator, RpiR family (NCBI ptt file) True
CAC0637 tyrS CDS None chromosome 741074 742297 + Tyrosyl-tRNA synthetase (NCBI ptt file) False
CAC0672 CAC0672 CDS None chromosome 779748 781409 + Fision threonyl-tRNA synthetase (N-terminal part) and uridine kinase (NCBI ptt file) False
CAC0673 CAC0673 CDS None chromosome 781431 782114 + L-serine dehydratase, beta chain (NCBI ptt file) False
CAC0904 CAC0904 CDS None chromosome 1034477 1036735 - ATPase with chaperon activity, two ATP-binding domains, ClpC orthologs (NCBI ptt file) False
CAC1295 CAC1295 CDS None chromosome 1438023 1438913 + ERA GTPase (NCBI ptt file) False
CAC1302 CAC1302 CDS None chromosome 1445787 1446476 + Predicted SAM-dependent methyltransferase (NCBI ptt file) False
CAC1404 CAC1404 CDS None chromosome 1547695 1548432 + Transcriptional regulator of sugar metabolism (deoR family) (NCBI ptt file) True
CAC1416 CAC1416 CDS None chromosome 1561646 1562161 + Predicted acetyltransferase (NCBI ptt file) False
CAC1622 CAC1622 CDS None chromosome 1761759 1762631 + Pyridoxal kinase related protein (NCBI ptt file) False
CAC1624 CAC1624 CDS None chromosome 1763428 1764270 + Uncharacterized protein from DegV (B.subtilis) family (NCBI ptt file) False
CAC1679 CAC1679 CDS None chromosome 1829759 1830019 + Hypothetical protein (NCBI ptt file) False
CAC1796 CAC1796 CDS None chromosome 1945792 1946811 + Predicted membrane-associated Zn-dependent protease (NCBI ptt file) False
CAC1849 CAC1849 CDS None chromosome 2001456 2002637 - Predicted flavoprotein, YhiN family (NCBI ptt file) False
CAC1850 CAC1850 CDS None chromosome 2002701 2003582 - Transcriptional regulators, RpiR family (NCBI ptt file) True
CAC1851 CAC1851 CDS None chromosome 2003729 2004439 - Predicted pseudouridylate synthase (NCBI ptt file) False
CAC1857 CAC1857 CDS None chromosome 2007736 2009106 - Predicted metal-dependent peptidase (NCBI ptt file) False
CAC1858 CAC1858 CDS None chromosome 2009103 2010236 - MoxR-like ATPase (NCBI ptt file) False
CAC1859 CAC1859 CDS None chromosome 2010248 2010886 - Hypothetical protein (NCBI ptt file) False
CAC2052 CAC2052 CDS None chromosome 2158772 2159485 - DNA-dependent RNA polymerase sigma subunit (NCBI ptt file) True
CAC2053 CAC2053 CDS None chromosome 2159469 2160059 - Hypothetical protein (NCBI ptt file) True
CAC2063 dacF CDS None chromosome 2166635 2167849 - D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) False
CAC2085 CAC2085 CDS None chromosome 2185906 2186301 - Uncharacterized protein from alkaline shock protein family, YQHY B.subtilis ortholog (NCBI ptt file) False
CAC2665 CAC2665 CDS None chromosome 2781575 2782180 - Xanthosine triphosphate pyrophosphatase, HAM1-like protein (NCBI ptt file) False
CAC2677 CAC2677 CDS None chromosome 2795526 2796239 - Lytic murein transglycosylase (NCBI ptt file) False

Genes Help

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Comments for Module 64

Please add your comments for this module by using the form below. Your comments will be publicly available.

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Social Help

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Module Overview

The landing module page shows quick summary info including co-expression profiles, de-novo identified motifs, and transcription factors and/or environmental factors as regulatory influences. It also includes module residual, motif e-values, conditions and links to other resources such as NCBI and Microbesonline. . If a transcription factor is included in the manually curated RegPrecise database, further information from RegPrecise is shown, allowing users to perform comparative analysis.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Network

A network view of the module is created using cytoscapeWeb and enables dynamic, interactive exploration of the module properties. In this view, module member genes, motifs, and regulatory influences are represented as peripheral nodes connected to core module node via edges. Module members are green circles, regulators are red triangles and motifs are blue diamonds. Selection of a node gives access to detailed information in a pop-up window, which allows dragging and pinning to compare multiple selections. Selecting module members will show information about the selected gene such as name, species and fucntions. Motif selection will show motif logo image and e-values. Bicluster selction will show expression profile and summary statistics for the module.

GeneModule member RegulatorRegulator MotifMotif

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

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.

Functions

Biological networks contain sets of regulatory units called functional modules that together play a role in regulation of specific functional processes. Connections between different modules in the network can help identify regulatory relationships such as hierarchy and epistasis. In addition, associating functions with modules enables putative assignment of functions to hypothetical genes. It is therefore essential to identify functional enrichment of modules within the regulatory network.

Functional annotations from single sources are often either not available or not complete. Therefore, we integrated KEGG pathway, Gene Ontology, TIGRFam and COG information as references for functional enrichment analysis.

We use hypergeometric p-values to identify significant overlaps between co-regulated module members and genes assigned to a particular functional annotation category. P-values are corrected for multiple comparisons by using Benjamini-Hochberg correction and filtered for p-values ≤ 0.05.

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.

Genes

Gene member table shows all the genes included in the module. Listed attributes are;

  1. Name: Gene name or Locus tag
  2. Common Name: Gene short name
  3. Type: Type of the feature, usually CDS.
  4. Gene ID: Link to NCBI Gene ID
  5. Chromosome: Chromosome name from annotation file
  6. Start/End:Feature start and end coordinates
  7. Strand: strand of the gene
  8. Description: Description of the gene from annotation file
  9. TF: If the gene is a Transcription Factor or not.

If you are browsing the Network Portal by using Gaggle/Firegoose, firegoose plugin will capture the NameList of the gene members. Captured names can be saved into your Workspace by clicking on "Capture" in the firegoose toolbar or can be directly sent other desktop and web resources by using "Broadcast" option.

Social

You can start a conversation about this module or join the existing discussion by adding your comments. In order to be able to add your comments you need to sign in by using any of the following services;Disqus, Google, Facebook or Twitter. For full compatibility with other network portal features, we recommend using your Google ID.

Definitions

Residual: is a measure of bicluster quality. Mean bicluster residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better bicluster quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

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.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by camparing to different functional categories such as KEGG, COG, GO etc. by using hypergeometric function. If the module is significantly enriched for any of the functions, this column will list few of the these functions as an overview. Full list of functions is available upon visiting the module page under the Functions tab.