Organism : Clostridium acetobutylicum | Module List:
Module 283 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 283

There are 11 regulatory influences for Module 283

Regulator Table (11)
Regulator Name Type
CAC0201 tf
CAC0768 tf
CAC2486 tf
CAC2084 tf
CAC1915 tf
CAC3673 tf
CAC3216 tf
CAC0951 tf
CAC0627 tf
CAC3466 tf
CAC2962 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
7218 2.50e+01 AAgtGGGgaaGaAgg
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7219 4.10e+01 aggaAttAtacgagG.gcGAT
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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 283 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell envelope tigr mainrole 2.52e-04 5.15e-04 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 8.58e-03 1.49e-02 10/31
Transcription cog subcategory 3.82e-03 6.98e-03 6/31
General function prediction only cog subcategory 2.00e-02 3.29e-02 6/31
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 283

There are 31 genes in Module 283

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0002 dnaN CDS None chromosome 2064 3164 + DNA polymerase III beta subunit (NCBI ptt file) False
CAC0010 CAC0010 CDS None chromosome 15826 18546 + Uncharacterized conserved protein, possible metal-binding (NCBI ptt file) False
CAC0174 CAC0174 CDS None chromosome 197025 197666 - Response regulator, CheY-like receiver domain and HTH DNA-binding domain (NCBI ptt file) True
CAC0282 CAC0282 CDS None chromosome 321564 322850 - Cytosine/guanine deaminase related protein (NCBI ptt file) False
CAC0458 CAC0458 CDS None chromosome 528231 529460 - Permease (NCBI ptt file) False
CAC0627 CAC0627 CDS None chromosome 729593 730027 + Transcriptional regulator, MarR/EmrR family (NCBI ptt file) True
CAC0728 CAC0728 CDS None chromosome 842425 843243 + SAM-dependent methyltransferase (NCBI ptt file) False
CAC1292 CAC1292 CDS None chromosome 1434585 1436672 + Membrane protein containing HD superfamily hydrolase domain, YQFF ortholog (NCBI ptt file) False
CAC1419 CAC1419 CDS None chromosome 1563321 1564187 + Uncharacterized proteins, homologs of microcin C7 resistance protein MccF (NCBI ptt file) False
CAC1542 CAC1542 CDS None chromosome 1687046 1687354 + Predicted membrane protein (NCBI ptt file) False
CAC1651 CAC1651 CDS None chromosome 1790629 1791864 - Predicted GTPase with uncharacterized domain, ortholog of T.maritima (4980952) (NCBI ptt file) False
CAC1749 CAC1749 CDS None chromosome 1895563 1896639 + BioB/LipA-like protein (NCBI ptt file) False
CAC2116 CAC2116 CDS None chromosome 2209025 2209627 - General stress protein, DnaK suppressor DskA, YTEA B.subtilis ortholog (NCBI ptt file) False
CAC2129 murE CDS None chromosome 2218962 2220410 - UDP-N-acetylmuramyl tripeptide synthase, MurE (NCBI ptt file) False
CAC2169 CAC2169 CDS None chromosome 2259162 2260244 - UDP-galactopyranose mutase (NCBI ptt file) False
CAC2170 CAC2170 CDS None chromosome 2260291 2260776 - Predicted membrane protein (NCBI ptt file) False
CAC2231 murG CDS None chromosome 2323781 2324860 - Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase, MurG (NCBI ptt file) False
CAC2410 recX CDS None chromosome 2527627 2528271 - Uncharacterized protein recX (NCBI ptt file) False
CAC2413 CAC2413 CDS None chromosome 2530721 2531221 - Predicted membrane protein (NCBI ptt file) False
CAC2414 CAC2414 CDS None chromosome 2531318 2532901 - Uncharacterized conserved protein, related to alpha-amylase/alpha-mannosidase (NCBI ptt file) False
CAC3089 CAC3089 CDS None chromosome 3243551 3243928 - Hypothetical protein (NCBI ptt file) False
CAC3185 CAC3185 CDS None chromosome 3322907 3324013 - Membrane-associated protein containing a homolog of PilT-like ATPase N-terminal domain, YACL B.subtilis ortholog (NCBI ptt file) False
CAC3203 hprT CDS None chromosome 3349730 3350266 - Hypoxanthine-guanine phosphoribosyltransferase (NCBI ptt file) False
CAC3207 CAC3207 CDS None chromosome 3355329 3355601 - Hypothetical protein (NCBI ptt file) False
CAC3216 mfd CDS None chromosome 3362265 3365780 - Transcription-repair coupling factor, MFD (superfamily II helicase ) (NCBI ptt file) True
CAC3400 CAC3400 CDS None chromosome 3583781 3584749 - Predicted dehydrogenase (NCBI ptt file) False
CAC3465 CAC3465 CDS None chromosome 3663710 3664246 - Amidase from nicotinamidase family (NCBI ptt file) False
CAC3466 CAC3466 CDS None chromosome 3664373 3665251 + Transcriptional regulator, LysR family (NCBI ptt file) True
CAC3467 CAC3467 CDS None chromosome 3665321 3666205 + Uncharacterized conserved protein, phnB family (NCBI ptt file) False
CAC3657 CAC3657 CDS None chromosome 3858980 3860428 + NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) False
CAC3673 xylR CDS None chromosome 3874104 3875261 - XylR transcriptional regulator (NCBI ptt file) True

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 283

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.