Organism : Clostridium acetobutylicum | Module List:
Module 291 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 291

There are 15 regulatory influences for Module 291

Regulator Table (15)
Regulator Name Type
CAC2471 tf
CAC1046 tf
CAC0240 tf
CAC1355 tf
CAC2473 tf
CAC0078 tf
CAC3579 tf
CAC0144 tf
CAC2818 tf
CAC0559 tf
CAC3646 tf
CAC0599 tf
CAC3525 tf
CAC0284 tf
CAC3349 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
7234 8.90e+02 ggggcCGAc.g
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7235 2.70e-01 AggaGG
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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 291 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 5.30e-05 1.24e-04 4/23
Riboflavin, FMN, and FAD tigr sub1role 0.00e+00 0.00e+00 3/23

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 8.36e-03 1.45e-02 8/23
Coenzyme transport and metabolism cog subcategory 9.90e-05 2.59e-04 5/23
General function prediction only cog subcategory 3.53e-03 6.49e-03 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 291

There are 23 genes in Module 291

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0511 CAC0511 CDS None chromosome 587659 588543 + Predicted P-loop containing kinase, similar to B.subtilis yvcJ (NCBI ptt file) False
CAC0535 CAC0535 CDS None chromosome 621428 622234 + Metal-dependent hydrolase of the beta-lactamase superfamily II (NCBI ptt file) False
CAC0590 ribD CDS None chromosome 682526 683677 + Riboflavin biosynthesis protein RIBD (pirimidine deaminase and pirimidine reductase) (NCBI ptt file) False
CAC0591 ribB CDS None chromosome 683684 684325 + Riboflavin synthase alpha chain (NCBI ptt file) False
CAC0592 ribA CDS None chromosome 684366 685571 + Riboflavin biosynthes protein RIBA (GTPcyclohydrolase/3,4-dihydroxy-2-butanone 4-phosphate synthase) (NCBI ptt file) False
CAC0593 ribH CDS None chromosome 685588 686055 + Riboflavin synthase beta-chain (NCBI ptt file) False
CAC0595 CAC0595 CDS None chromosome 687014 687574 + Glutamine amidotranspherase (possibly involved in histidine and purine biosinthesis) (NCBI ptt file) False
CAC0599 CAC0599 CDS None chromosome 691644 692021 + Transcriptional regulator, GntR family (NCBI ptt file) True
CAC0749 CAC0749 CDS None chromosome 871872 872774 + HD hydrolase superfamily protein (NCBI ptt file) False
CAC1636 CAC1636 CDS None chromosome 1778324 1778710 + Uncharacterized protein, homolog of B. firmus (2654481) (NCBI ptt file) False
CAC1638 CAC1638 CDS None chromosome 1779028 1779300 + Hypothetical protein, CF-37 family(almost identical) (NCBI ptt file) False
CAC1639 CAC1639 CDS None chromosome 1779297 1780196 + Hypothetical protein, CF-7 family (NCBI ptt file) False
CAC1640 CAC1640 CDS None chromosome 1780108 1781241 + Uncharacterized protein, YQCG B.subtilis homolog; CF-7 family (NCBI ptt file) False
CAC1671 CAC1671 CDS None chromosome 1814785 1816050 + Predicted ATPase related to the helicase subunit of the Holliday junction resolvase (NCBI ptt file) False
CAC1672 CAC1672 CDS None chromosome 1816050 1818425 + Rad3-related DNA helicase (NCBI ptt file) False
CAC1966 CAC1966 CDS None chromosome 2082172 2083506 - Surface-layer related glycoprotein (NCBI ptt file) False
CAC1969 CAC1969 CDS None chromosome 2084923 2086698 - Possible plasmid transfer factor, TraK (NCBI ptt file) False
CAC2541 CAC2541 CDS None chromosome 2649664 2650002 - Reductase/isomerase/elongation factor common domain (NCBI ptt file) False
CAC2544 etfB CDS None chromosome 2652820 2653608 - Electron-transferring flavoprotein small subunit (NCBI ptt file) False
CAC3350 CAC3350 CDS None chromosome 3523661 3524248 + Putative intracellular protease/amidase (ThiJ family) (NCBI ptt file) False
CAC3505 CAC3505 CDS None chromosome 3700449 3701021 - Multimeric flavodoxin WrbA family protein (NCBI ptt file) False
CAC3576 CAC3576 CDS None chromosome 3776151 3777083 - Dioxygenase related to 2-nitropropane dioxygenase (NCBI ptt file) False
CAC3656 CAC3656 CDS None chromosome 3858433 3858699 - Uncharacterized conserved protein, yaiN/yohL family (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 291

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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.