Organism : Clostridium acetobutylicum | Module List:
Module 335 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 335

There are 12 regulatory influences for Module 335

Regulator Table (12)
Regulator Name Type
CAC3142 tf
CAC0162 tf
CAC1300 tf
CAC3149 tf
CAC2430 tf
CAC0707 tf
CAC0863 tf
CAC1032 tf
CAC0933 tf
CAC1320 tf
CAC1832 tf
CAC3199 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
7322 1.20e-05 gGAGAGGatG
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7323 9.80e+02 GCCTTCACcCC
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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 335 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 0.00e+00 0.00e+00 6/23
ATP-proton motive force interconversion tigr sub1role 0.00e+00 0.00e+00 5/23
DNA metabolism tigr mainrole 4.25e-04 8.17e-04 3/23
DNA replication, recombination, and repair tigr sub1role 3.02e-04 6.02e-04 3/23
Transcription tigr mainrole 1.00e-05 2.80e-05 3/23

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 3.00e-06 1.20e-05 12/23
Translation, ribosomal structure and biogenesis cog subcategory 4.16e-04 8.88e-04 5/23
Replication, recombination and repair cog subcategory 1.08e-03 2.11e-03 4/23
Energy production and conversion cog subcategory 6.00e-06 2.50e-05 6/23
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 335

There are 23 genes in Module 335

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0502 uvrB CDS None chromosome 575260 577260 + Excinuclease ABC subunit B (helicase subunit of the DNA excision repair complex) (NCBI ptt file) False
CAC0503 uvrA CDS None chromosome 577260 580079 + Excinuclease ABC subunit A (ATP-ase), (uvrA) (NCBI ptt file) False
CAC0710 pgk CDS None chromosome 822356 823549 + 3-phosphoglycerate kinase (NCBI ptt file) False
CAC1735 CAC1735 CDS None chromosome 1882052 1883695 + Predicted kinase related to hydroxyacetone kinase, YLOV ortholog (NCBI ptt file) False
CAC1743 askA CDS None chromosome 1891302 1892507 + Acetate kinase (NCBI ptt file) False
CAC1748 rncS CDS None chromosome 1894870 1895562 + DsRNA-specific ribonuclease III (NCBI ptt file) False
CAC2411 CAC2411 CDS None chromosome 2528273 2529523 - Zn-dependent protease of MPP family (NCBI ptt file) False
CAC2845 prfB CDS None chromosome 2976659 2977648 - Protein chain release factor B (NCBI ptt file) False
CAC2864 atpC CDS None chromosome 2998857 2999258 - FoF1-type ATP synthase epsilon subunit (NCBI ptt file) False
CAC2866 atpG CDS None chromosome 3000685 3001533 - FoF1-type ATP synthase gamma subunit (NCBI ptt file) False
CAC2867 atpA CDS None chromosome 3001565 3003082 - FoF1-type ATP synthase alpha subunit (NCBI ptt file) False
CAC2868 atpH CDS None chromosome 3003093 3003632 - FoF1-type ATP synthase delta subunit (NCBI ptt file) False
CAC2869 atpF CDS None chromosome 3003635 3004114 - FoF1-type ATP synthase B subunit (NCBI ptt file) False
CAC3017 CAC3017 CDS None chromosome 3158795 3159643 + Predicted xylanase/chitin deacetylase (NCBI ptt file) False
CAC3112 adk CDS None chromosome 3258846 3259493 - Adenylate kinase (NCBI ptt file) False
CAC3114 rplO CDS None chromosome 3260799 3261239 - Ribosomal protein L15 (NCBI ptt file) False
CAC3120 rpsN CDS None chromosome 3263342 3263527 - Ribosomal protein S14 (NCBI ptt file) False
CAC3136 tufA CDS None chromosome 3270300 3271493 - Elongation Factor Tu (Ef-Tu) (NCBI ptt file) False
CAC3138 fus CDS None chromosome 3271523 3273586 - Translation elongation factor EF-G (NCBI ptt file) False
CAC3142 rpoC CDS None chromosome 3275271 3278819 - DNA-dependent RNA polymerase beta' subunit (NCBI ptt file) True
CAC3143 rpoB CDS None chromosome 3278841 3282566 - DNA-dependent RNA polymerase beta subunit (NCBI ptt file) True
CAC3563 CAC3563 CDS None chromosome 3761256 3762989 - Mismatch repair protein MutS-like ATPase (NCBI ptt file) False
CAC3715 dnaC CDS None chromosome 3920086 3921414 - Replicative DNA helicase, DNAC (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.