Organism : Clostridium acetobutylicum | Module List:
Module 29 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 29

There are 12 regulatory influences for Module 29

Regulator Table (12)
Regulator Name Type
CAC2306 tf
CAC1799 tf
CAC0949 tf
CAC1670 tf
CAC1467 tf
CAC2242 tf
CAC2307 tf
CAC1945 tf
CAC3507 tf
CAC1264 tf
CAC0289 tf
CAC3649 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
6712 1.40e-12 AGggGgg
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6713 5.70e+03 GCGGGac
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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 29 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Unknown function tigr mainrole 3.21e-03 4.90e-03 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.06e-02 1.81e-02 9/26
Cell cycle control, cell division, chromosome partitioning cog subcategory 1.00e-04 2.61e-04 3/26
Amino acid transport and metabolism cog subcategory 4.05e-03 7.39e-03 5/26
Inorganic ion transport and metabolism cog subcategory 9.87e-03 1.70e-02 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 29

There are 26 genes in Module 29

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0007 gyrA CDS None chromosome 6783 9275 + DNA gyrase (topoisomerase II) A subunit (NCBI ptt file) False
CAC0302 CAC0302 CDS None chromosome 357210 357413 + Predicted metal-binding protein of ferredoxin fold (NCBI ptt file) False
CAC0489 CAC0489 CDS None chromosome 563156 563530 + Holo-acyl-carrier protein synthase (NCBI ptt file) False
CAC0490 CAC0490 CDS None chromosome 563532 565040 + Predicted sugar kinase, N-terminal region - uncharacterized conserved protein (NCBI ptt file) False
CAC0882 CAC0882 CDS None chromosome 1011286 1011930 + Predicted membrane protein, hemolysin III homolog (NCBI ptt file) False
CAC0949 CAC0949 CDS None chromosome 1088983 1089429 + Predicted transcriptional regulator (NCBI ptt file) True
CAC1053 CAC1053 CDS None chromosome 1208215 1209615 + LPS glycosyltransferase (NCBI ptt file) False
CAC1286 CAC1286 CDS None chromosome 1430516 1431826 + Fe-S oxidoreductases (NCBI ptt file) False
CAC1586 CAC1586 CDS None chromosome 1730509 1730928 + Integral membrane protein possibly involved in chromosome condensation (NCBI ptt file) False
CAC1625 CAC1625 CDS None chromosome 1764289 1764948 + Phosphoserine phosphatase family protein (NCBI ptt file) False
CAC1674 gltB CDS None chromosome 1823115 1824554 + Small subunit of NADPH-dependent glutamate synthase (NCBI ptt file) False
CAC1692 ftsA CDS None chromosome 1843404 1844660 + Cell division protein, ftsA (NCBI ptt file) False
CAC1750 CAC1750 CDS None chromosome 1896696 1896956 + SpoVS-related protein (NCBI ptt file) False
CAC1752 ftsY CDS None chromosome 1900778 1901689 + Signal recognition particle GTPase, FtsY (NCBI ptt file) False
CAC1812 CAC1812 CDS None chromosome 1960690 1962987 + Sporulation protein SpoIIIE, DNA segregation ATPase (NCBI ptt file) False
CAC1831 CAC1831 CDS None chromosome 1982704 1983090 - Protein containing Zn-finger domain (NCBI ptt file) False
CAC2130 spoVD CDS None chromosome 2220690 2222879 - Stage V sporulation protein D, spoVD, FtsI/pbp family (NCBI ptt file) False
CAC2308 spoIIAA CDS None chromosome 2410990 2411325 - Anti-anti-sigma factor (antagonist of SpoIIAB) (NCBI ptt file) False
CAC2507 CAC2507 CDS None chromosome 2616406 2616612 - Predicted membrane protein (NCBI ptt file) False
CAC2508 CAC2508 CDS None chromosome 2616627 2617175 - Nitroreductase family protein (NCBI ptt file) False
CAC2584 CAC2584 CDS None chromosome 2688963 2690408 - Protein containing ChW-repeats (NCBI ptt file) False
CAC2660 pykA CDS None chromosome 2773031 2776465 - Pyruvate carboxylase, PYKA (NCBI ptt file) False
CAC3176 ilvN CDS None chromosome 3312119 3312616 - Acetolactate synthase, small subunit (NCBI ptt file) False
CAC3319 CAC3319 CDS None chromosome 3491524 3492861 + Signal transduction histidine kinase (NCBI ptt file) False
CAC3630 oppC CDS None chromosome 3830428 3831348 - Oligopeptide ABC transporter, permease component (NCBI ptt file) False
CAC3631 oppB CDS None chromosome 3831360 3832292 - Oligopeptide ABC transporter, permease component (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.

Comments for Module 29

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.