Organism : Clostridium acetobutylicum | Module List:
Module 51 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 51

There are 11 regulatory influences for Module 51

Regulator Table (11)
Regulator Name Type
CAC2084 tf
CAC1264 tf
CAC2074 tf
CAC0113 tf
CAC0859 tf
CAC3611 tf
CAC1786 tf
CAC1226 tf
CAC2060 tf
CAC2209 tf
CAC2608 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
6756 5.80e-03 taaGGagG
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6757 2.00e+03 GGACCTGG
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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 51 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 9.50e-05 2.12e-04 4/30
DNA replication, recombination, and repair tigr sub1role 8.65e-04 1.53e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 3.73e-03 6.82e-03 4/30
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 51

There are 30 genes in Module 51

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC1292 CAC1292 CDS None chromosome 1434585 1436672 + Membrane protein containing HD superfamily hydrolase domain, YQFF ortholog (NCBI ptt file) False
CAC1293 CAC1293 CDS None chromosome 1436690 1437190 + Uncharacterized conserved predicted metal-binding protein, YQFG ortholog (NCBI ptt file) False
CAC1294 dgkA/pgpB CDS None chromosome 1437216 1437914 + Diacylglycerol kinase (dgkA) fused to phosphatase B domain (pgpB) (NCBI ptt file) False
CAC1305 CAC1305 CDS None chromosome 1449041 1450537 + Uncharacterized protein similar to a protein from Cylindrotheca fusiformis plasmid (GI:99322) (NCBI ptt file) False
CAC1306 CAC1306 CDS None chromosome 1450553 1451041 + Hypothetical protein (NCBI ptt file) False
CAC1307 CAC1307 CDS None chromosome 1451159 1451308 + Hypothetical protein (NCBI ptt file) False
CAC1308 CAC1308 CDS None chromosome 1451767 1452360 + Uncharacterized low-complexity protein, related to YISX/YYBG B.subtilis (NCBI ptt file) False
CAC1309 CAC1309 CDS None chromosome 1439080 1439736 + Hypothetical protein (NCBI ptt file) False
CAC1625 CAC1625 CDS None chromosome 1764289 1764948 + Phosphoserine phosphatase family protein (NCBI ptt file) False
CAC1736 recG CDS None chromosome 1883855 1885891 + RecG helicase (NCBI ptt file) False
CAC1794 CAC1794 CDS None chromosome 1943649 1944605 + Predicted permease (NCBI ptt file) False
CAC1818 CAC1818 CDS None chromosome 1968553 1969425 + Conserved membrane protein, possible 4-hydroxybenzoate octaprenyltranferase (NCBI ptt file) False
CAC1823 CAC1823 CDS None chromosome 1973730 1974035 + Uncharacterized conserved protein (NCBI ptt file) False
CAC1824 clpA CDS None chromosome 1974039 1976291 + ATP-dependent Clp proteinase (NCBI ptt file) False
CAC1982 CAC1982 CDS None chromosome 2095720 2097183 + Predicted membrane protein (NCBI ptt file) False
CAC2065 deoB CDS None chromosome 2168794 2169966 - Phosphopentomutase (NCBI ptt file) False
CAC2066 CAC2066 CDS None chromosome 2170033 2170911 - Integrase/recombinase XerD family (NCBI ptt file) False
CAC2067 CAC2067 CDS None chromosome 2170932 2171159 - Hypothetical protein (NCBI ptt file) False
CAC2068 CAC2068 CDS None chromosome 2171159 2171806 - Sporulation factor spoIIM, uncharacterized membrane protein (NCBI ptt file) False
CAC2115 lspA CDS None chromosome 2208465 2208929 - Lipoprotein signal peptidase (NCBI ptt file) False
CAC2138 CAC2138 CDS None chromosome 2231895 2232827 + Exopolyphosphatase (NCBI ptt file) False
CAC2234 nifS CDS None chromosome 2327863 2328993 - NifS family enzyme (cysteine desulfurase/cysteine sulfinate desulfinase) (NCBI ptt file) False
CAC2269 aspS CDS None chromosome 2371732 2373519 - Aspartyl-tRNA synthetase (NCBI ptt file) False
CAC2340 mutS1 CDS None chromosome 2448638 2451004 - DNA mismatch repair protein mutS, YSHD B.subtilis ortholog (NCBI ptt file) False
CAC2341 CAC2341 CDS None chromosome 2451006 2453369 - Collagenase family protease (NCBI ptt file) False
CAC2724 CAC2724 CDS None chromosome 2849739 2850212 - Hypothetical protein (NCBI ptt file) False
CAC2725 CAC2725 CDS None chromosome 2850222 2851214 - Predicted hydrolase from alpha/beta family, YQKD B.subtilis ortholog (NCBI ptt file) False
CAC2770 CAC2770 CDS None chromosome 2901561 2901980 - Amino acid transporter (NCBI ptt file) False
CAC3390 CAC3390 CDS None chromosome 3573536 3574648 - Response regulator (CheY-like receiver domain containing) (NCBI ptt file) False
CAC3391 CAC3391 CDS None chromosome 3574667 3576406 - Membrane associated signal transduction histidine kinase (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 51

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.