Organism : Clostridium acetobutylicum | Module List:
Module 91 Profile

GeneModule member RegulatorRegulator MotifMotif
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 91

There are 6 regulatory influences for Module 91

Regulator Table (6)
Regulator Name Type
CAC2297 tf
CAC3166 tf
CAC2143 tf
CAC3361 tf
CAC3729 tf
CAC2476 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
6836 7.00e-06 AGGagggg
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6837 7.90e+03 CTaGCCaCC
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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 91 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Fatty acid and phospholipid metabolism tigr mainrole 9.00e-06 2.60e-05 3/26
Biosynthesis tigr sub1role 7.00e-06 2.10e-05 3/26
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 2.03e-04 4.22e-04 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Lipid transport and metabolism cog subcategory 1.12e-03 2.19e-03 3/26
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 91

There are 26 genes in Module 91

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0224 CAC0224 CDS None chromosome 248980 249651 + Response regulator (CheY-like receiver domain and HTH DNA-binding domain) (NCBI ptt file) False
CAC0229 CAC0229 CDS None chromosome 259648 261075 + Predicted Zn-dependent proteases, TLDD ortholog (NCBI ptt file) False
CAC0230 CAC0230 CDS None chromosome 261075 262373 + Inactivated predicted Zn-dependent protease, PMBA ortholog (NCBI ptt file) False
CAC0290 CAC0290 CDS None chromosome 329029 330432 + Sensory transduction histidine kinases (NCBI ptt file) False
CAC0400 CAC0400 CDS None chromosome 463562 463813 + Hypothetical protein, CF-19 family (NCBI ptt file) False
CAC0602 ftsH CDS None chromosome 695723 697588 + ATP-dependent zinc metallopeptidase FtsH (cell dividion protein) (NCBI ptt file) False
CAC0603 CAC0603 CDS None chromosome 697543 699708 + Superfamily I DNA and RNA helicase (NCBI ptt file) False
CAC0764 CAC0764 CDS None chromosome 886021 887256 + NADPH-dependent glutamate synthase beta chain (NCBI ptt file) False
CAC1540 CAC1540 CDS None chromosome 1685144 1686130 + Uncharacterized ATP-grasp enzyme (NCBI ptt file) False
CAC1544 CAC1544 CDS None chromosome 1688808 1689206 + Cytidine deaminase, cdd (NCBI ptt file) False
CAC1546 deoA CDS None chromosome 1689969 1691270 + Pyrimidine-nucleoside phosphorylase (NCBI ptt file) False
CAC1717 CAC1717 CDS None chromosome 1866997 1867275 + Uncharacterized conserved protein, YLOA ortholog (NCBI ptt file) False
CAC1796 CAC1796 CDS None chromosome 1945792 1946811 + Predicted membrane-associated Zn-dependent protease (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
CAC2296 CAC2296 CDS None chromosome 2398957 2399601 - Uncharacterized protein, YigZ family (NCBI ptt file) False
CAC2297 CAC2297 CDS None chromosome 2399636 2401039 - Transcriptional regulator of MocR family (DNA-binding HTH domain and aminotransferase domain) (NCBI ptt file) True
CAC2298 CAC2298 CDS None chromosome 2401052 2401948 - Predicted nucleotidyltransferase (NCBI ptt file) False
CAC2340 mutS1 CDS None chromosome 2448638 2451004 - DNA mismatch repair protein mutS, YSHD B.subtilis ortholog (NCBI ptt file) False
CAC2415 CAC2415 CDS None chromosome 2533043 2533537 - Uncharacterized conserved protein (NCBI ptt file) False
CAC2736 sbcC CDS None chromosome 2861388 2864879 - ATPase involved in DNA repair (NCBI ptt file) False
CAC3299 bdhA CDS None chromosome 3464035 3465204 - NADH-dependent butanol dehydrogenase A (BDH I) (NCBI ptt file) False
CAC3392 CAC3392 CDS None chromosome 3576543 3577703 - NADH-dependent butanol dehydrogenase (NCBI ptt file) False
CAC3571 fabZ CDS None chromosome 3772226 3772651 - Hydroxymyristoyl-(acyl carrier protein) dehydratase (NCBI ptt file) False
CAC3572 accB CDS None chromosome 3772672 3773151 - Biotin carboxyl carrier protein of acetyl-CoA carboxylase (NCBI ptt file) False
CAC3577 acp CDS None chromosome 3777142 3777372 - Acyl Carrier Protein, ACP (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.

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.