Organism : Clostridium acetobutylicum | Module List:
Module 286 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 286

There are 12 regulatory influences for Module 286

Regulator Table (12)
Regulator Name Type
CAC3579 tf
CAC0768 tf
CAC1941 tf
CAC0549 tf
CAC2616 tf
CAC3236 tf
CAC1753 tf
CAC3224 tf
CAC0977 tf
CAC3143 tf
CAC2084 tf
CAC3216 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
7224 3.40e+01 aaGgAGg
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7225 5.50e+03 CAGaGGGG
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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 286 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 9.74e-03 1.68e-02 11/25
Cell wall/membrane/envelope biogenesis cog subcategory 1.01e-03 1.99e-03 5/25
Amino acid transport and metabolism cog subcategory 3.28e-03 6.05e-03 5/25
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 286

There are 25 genes in Module 286

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0114 CAC0114 CDS None chromosome 124880 125407 + Predicted membrane protein (NCBI ptt file) False
CAC0150 CAC0150 CDS None chromosome 154868 155533 - Hypothetical protein (NCBI ptt file) False
CAC0379 CAC0379 CDS None chromosome 441794 442444 + Transcriptional regulator, GntR family (NCBI ptt file) True
CAC0458 CAC0458 CDS None chromosome 528231 529460 - Permease (NCBI ptt file) False
CAC0476 pepT CDS None chromosome 549510 550736 + Peptidase T (aminotripeptidase), gene pepT (NCBI ptt file) False
CAC0519 pyrC CDS None chromosome 598982 600256 + Dihydroorotase (NCBI ptt file) False
CAC0688 CAC0688 CDS None chromosome 794546 795265 + 1-acyl-sn-glycerol-3-phosphate acyltransferase (NCBI ptt file) False
CAC1299 dnaG CDS None chromosome 1441801 1443591 + DNA primase, DNAG (NCBI ptt file) False
CAC1489 CAC1489 CDS None chromosome 1636159 1636818 - Protein of phosphatidic acid phosphatase family, YNBD E.coli ortholog (NCBI ptt file) False
CAC2095 CAC2095 CDS None chromosome 2192448 2193518 - Aminopeptidase P AMPP/PEPQ family enzyme, YQHT B.subtilis ortholog (NCBI ptt file) False
CAC2117 pfs CDS None chromosome 2209720 2210412 - Nucleoside phosphorylase (NCBI ptt file) False
CAC2169 CAC2169 CDS None chromosome 2259162 2260244 - UDP-galactopyranose mutase (NCBI ptt file) False
CAC2183 CAC2183 CDS None chromosome 2275062 2275235 - Uncharacterized protein, posible homoloh of YJFB B. subtilis (NCBI ptt file) False
CAC2227 CAC2227 CDS None chromosome 2317702 2318343 - Phosphoserine phosphatase family enzyme (NCBI ptt file) False
CAC2231 murG CDS None chromosome 2323781 2324860 - Undecaprenyl-PP-MurNAc-pentapeptide-UDPGlcNAc GlcNAc transferase, MurG (NCBI ptt file) False
CAC2264 glyA CDS None chromosome 2368162 2369397 - Glycine hydroxymethyltransferase (NCBI ptt file) False
CAC2680 pgi CDS None chromosome 2800720 2802072 - Glucose-6-phosphate isomerase (NCBI ptt file) False
CAC2771 CAC2771 CDS None chromosome 2901999 2902952 - Amino acid transporter (NCBI ptt file) False
CAC2854 recD CDS None chromosome 2987112 2989331 - ATP-dependent exoDNAse (exonuclease V), alpha subunit, RecD (NCBI ptt file) False
CAC2897 CAC2897 CDS None chromosome 3031250 3032404 + Predicted UDP-glucuronosyltransferase, YPFP B/subtilis ortholog (NCBI ptt file) False
CAC2917 CAC2917 CDS None chromosome 3051540 3052358 - acetyl esterase family enzyme (NCBI ptt file) False
CAC2925 CAC2925 CDS None chromosome 3058364 3058849 + HD superfamily hydrolase (NCBI ptt file) False
CAC2927 folA/folK CDS None chromosome 3059672 3060499 + Dihydroneopterin aldolase fused to 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (NCBI ptt file) False
CAC3072 CAC3072 CDS None chromosome 3222505 3223557 - Mannose-1-phosphate guanylyltransferase (NCBI ptt file) False
CAC3683 CAC3683 CDS None chromosome 3886867 3888882 + Penicillin-binding protein 2 (serine-type D-Ala-D-Ala carboxypeptidase) (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.