Organism : Clostridium acetobutylicum | Module List:
Module 282 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 282

There are 11 regulatory influences for Module 282

Regulator Table (11)
Regulator Name Type
CAC1070 tf
CAC3475 tf
CAC2074 tf
CAC3512 tf
CAC0081 tf
CAC3406 tf
CAC3649 tf
CAC0032 tf
CAC1766 tf
CAC2546 tf
CAC0360 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
7216 2.20e-02 AgGAGaG
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7217 1.10e+04 GCAGtaGAACAcC
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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 282 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Coenzyme transport and metabolism cog subcategory 2.89e-03 5.36e-03 4/29
Lipid transport and metabolism cog subcategory 1.71e-03 3.25e-03 3/29
Inorganic ion transport and metabolism cog subcategory 1.45e-02 2.44e-02 3/29
General function prediction only cog subcategory 1.39e-02 2.34e-02 6/29
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 282

There are 29 genes in Module 282

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0366 CAC0366 CDS None chromosome 425216 426121 + Predicted permease (NCBI ptt file) False
CAC0374 CAC0374 CDS None chromosome 436296 437612 + Similar to ABC transporter (permease) (NCBI ptt file) False
CAC0379 CAC0379 CDS None chromosome 441794 442444 + Transcriptional regulator, GntR family (NCBI ptt file) True
CAC0508 uvrC CDS None chromosome 583923 585794 + Excinuclease ABC subunit C (NCBI ptt file) False
CAC0522 CAC0522 CDS None chromosome 601719 602516 - Predicted hydrolase of the HAD superfamily (NCBI ptt file) False
CAC0640 CAC0640 CDS None chromosome 744715 745410 + Predicted phoshohydrolase (NCBI ptt file) False
CAC0676 pssA CDS None chromosome 783453 783992 - Phosphatidylserine synthase (NCBI ptt file) False
CAC1011 CAC1011 CDS None chromosome 1158427 1158843 + Uncharacterized small membrane protein, homolog of ykvA B.subtilis (NCBI ptt file) False
CAC1070 CAC1070 CDS None chromosome 1222444 1222860 - Transcriptional regulator, AcrR family (NCBI ptt file) True
CAC1407 CAC1407 CDS None chromosome 1551307 1553193 + PTS system, beta-glucosides-specific IIABC component (NCBI ptt file) False
CAC1593 CAC1593 CDS None chromosome 1737474 1738370 - Zn-binding lipoprotein related (surface adhesin A), ADHS (NCBI ptt file) False
CAC1659 CAC1659 CDS None chromosome 1803685 1803846 + Predicted membrane protein (NCBI ptt file) False
CAC1777 CAC1777 CDS None chromosome 1924913 1925836 + Nudix (MutT-like) hydrolase (NCBI ptt file) False
CAC1779 CAC1779 CDS None chromosome 1926699 1927073 + Hypothetical protein (NCBI ptt file) False
CAC1781 CAC1781 CDS None chromosome 1928572 1929177 + Predicted nucleotidyltransferase (NCBI ptt file) False
CAC1791 CAC1791 CDS None chromosome 1940512 1941285 + Undecaprenyl pyrophosphate synthase (NCBI ptt file) False
CAC1792 cdsA CDS None chromosome 1941285 1942022 + CDP-diglyceride synthetase (NCBI ptt file) False
CAC2022 moaB CDS None chromosome 2135557 2136054 - Molybdopterin biosynthesis enzyme, moaB (NCBI ptt file) False
CAC2025 CAC2025 CDS None chromosome 2136717 2137139 - Hypothetical protein (NCBI ptt file) False
CAC2100 CAC2100 CDS None chromosome 2195460 2195912 - Hypothetical protein (NCBI ptt file) False
CAC2104 CAC2104 CDS None chromosome 2197116 2198306 - General secretion pathway protein F (NCBI ptt file) False
CAC2106 CAC2106 CDS None chromosome 2199962 2200159 + Predicted membrane protein (NCBI ptt file) False
CAC2170 CAC2170 CDS None chromosome 2260291 2260776 - Predicted membrane protein (NCBI ptt file) False
CAC2226 CAC2226 CDS None chromosome 2316758 2317600 - Enzyme of ILVE/PABC family (branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase) (NCBI ptt file) False
CAC2292 CAC2292 CDS None chromosome 2396341 2396553 + Predicted membrane protein (NCBI ptt file) False
CAC2410 recX CDS None chromosome 2527627 2528271 - Uncharacterized protein recX (NCBI ptt file) False
CAC2442 CAC2442 CDS None chromosome 2559657 2560685 + Hemin permease (NCBI ptt file) False
CAC2443 CAC2443 CDS None chromosome 2560682 2561845 + Iron (III) ABC transporter, ATPase component (NCBI ptt file) False
CAC2444 CAC2444 CDS None chromosome 2561850 2562116 + Predicted metal-binding protein (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 282

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.