Organism : Clostridium acetobutylicum | Module List:
Module 254 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 254

There are 12 regulatory influences for Module 254

Regulator Table (12)
Regulator Name Type
CAC2113 tf
CAC0951 tf
CAC1753 tf
CAC2052 tf
CAC0841 tf
CAC3731 tf
CAC0115 tf
CAC1950 tf
CAC2608 tf
CAC3152 tf
CAC0766 tf
CAC3104 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
7160 5.30e+03 GGTGCG
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7161 1.60e-01 TaGgAgG
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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 254 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 1.73e-04 3.65e-04 3/25
Protein synthesis tigr mainrole 1.30e-05 3.70e-05 6/25
Ribosomal proteins: synthesis and modification tigr sub1role 1.50e-05 4.30e-05 4/25
Unknown function tigr mainrole 2.77e-03 4.30e-03 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 5.96e-03 1.06e-02 8/25
Translation, ribosomal structure and biogenesis cog subcategory 8.00e-06 3.50e-05 7/25
Nucleotide transport and metabolism cog subcategory 1.20e-03 2.33e-03 3/25
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 254

There are 25 genes in Module 254

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0027 pyrE CDS None chromosome 37376 38050 + Orotate phosphoribosyltranspherase (NCBI ptt file) False
CAC0523 CAC0523 CDS None chromosome 602657 604039 + SAM-dependent methyltransferase related to tRNA(uracyl-5-)-methyltransferase (trmA family) (NCBI ptt file) False
CAC0729 CAC0729 CDS None chromosome 843290 844636 - Hypothetical protein (NCBI ptt file) False
CAC0883 CAC0883 CDS None chromosome 1012076 1013422 + Probable cation efflux pump (multidrug resistance protein) (NCBI ptt file) False
CAC0885 CAC0885 CDS None chromosome 1014240 1014950 + Ferredoxin 3 fused to uncharacterized domain, orthologous of AF0155 from Archaeoglobus fulgidus (NCBI ptt file) False
CAC0991 CAC0991 CDS None chromosome 1138921 1139430 + Putative intracellular protease (NCBI ptt file) False
CAC1254 CAC1254 CDS None chromosome 1398754 1400622 + Fe-S oxidoreductase (NCBI ptt file) False
CAC1255 CAC1255 CDS None chromosome 1400591 1401307 + Uncharacterized conserved protein (NCBI ptt file) False
CAC1278 lepA CDS None chromosome 1420596 1422404 + Membrane GTPase lepA (NCBI ptt file) False
CAC1354 CAC1354 CDS None chromosome 1499695 1500174 + Phosphotransferase system IIA component (NCBI ptt file) False
CAC2368 CAC2368 CDS None chromosome 2479281 2479682 - Hypothetical protein (NCBI ptt file) False
CAC2369 CAC2369 CDS None chromosome 2479690 2480019 - Hypothetical protein (NCBI ptt file) False
CAC2648 CAC2648 CDS None chromosome 2761453 2762271 - Uncharacterized conserved membrane protein (NCBI ptt file) False
CAC2769 ppiB CDS None chromosome 2900960 2901484 - Peptidyl-prolyl cis-transisomerase, cyclophilin family (NCBI ptt file) False
CAC2892 ctrA CDS None chromosome 3025757 3027364 - CTP synthase (UTP-ammonia lyase) (NCBI ptt file) False
CAC2982 CAC2982 CDS None chromosome 3119141 3119974 - MinD family ATPase (chromosome partitioning) (NCBI ptt file) False
CAC2989 CAC2989 CDS None chromosome 3126129 3126890 - PHP superfamily hydrolase, YABD ortholog (NCBI ptt file) False
CAC3098 rplM CDS None chromosome 3250606 3251040 - Ribosomal protein L13 (NCBI ptt file) False
CAC3130 rplB CDS None chromosome 3267163 3267996 - Ribosomal protein L2 (NCBI ptt file) False
CAC3133 rplC CDS None chromosome 3268991 3269620 - Ribosomal protein L3 (NCBI ptt file) False
CAC3139 rpsG CDS None chromosome 3273758 3274228 - Ribosomal protein S7 (NCBI ptt file) False
CAC3140 rpsL CDS None chromosome 3274414 3274791 - Ribosomal protein S12 (NCBI ptt file) False
CAC3141 CAC3141 CDS None chromosome 3274884 3275123 - Ribosomal protein HS6-type (NCBI ptt file) False
CAC3593 purA CDS None chromosome 3795231 3796517 - Adenylosuccinate synthase (NCBI ptt file) False
CAC3732 gidB CDS None chromosome 3934488 3935207 - Glucose-inhibited division protein, GIDB (S-adenosylmethionine-dependent methyltransferase) (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.