Organism : Clostridium acetobutylicum | Module List:
Module 92 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 92

There are 12 regulatory influences for Module 92

Regulator Table (12)
Regulator Name Type
CAC2242 tf
CAC0459 tf
CAC0032 tf
CAC1928 tf
CAC0514 tf
CAC3525 tf
CAC0078 tf
CAC3424 tf
CAC0559 tf
CAC3361 tf
CAC0821 tf
CAC0745 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
6838 9.10e-02 AgGtagGC
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6839 1.50e+03 A.gGAGGA
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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 92 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 1.19e-04 2.61e-04 4/27
Heme, porphyrin, and cobalamin tigr sub1role 0.00e+00 0.00e+00 4/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 6.98e-03 1.23e-02 12/27
Energy production and conversion cog subcategory 1.68e-03 3.19e-03 4/27
Coenzyme transport and metabolism cog subcategory 2.60e-05 9.70e-05 6/27
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 92

There are 27 genes in Module 92

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0095 hemA CDS None chromosome 103870 105060 + Glutamil-tRNA reductase (NCBI ptt file) False
CAC0096 hemW CDS None chromosome 105024 105671 + Precorrin-2 dehydrogenase (NCBI ptt file) False
CAC0097 hemC CDS None chromosome 105680 106555 + Hydroxymrthylbilane syntase (porphobilinogen deaminase) (NCBI ptt file) False
CAC0098 hemD CDS None chromosome 106555 108027 + Uroporphyrinogen III syntase (NCBI ptt file) False
CAC0099 hemL CDS None chromosome 108017 109285 + Glutamate-1-semialdehyde aminotransferase (NCBI ptt file) False
CAC0100 hemB CDS None chromosome 109303 110265 + Delta-aminolevulinic acid dehydratase (porphobilinogen synthase) (NCBI ptt file) False
CAC0145 CAC0145 CDS None chromosome 150238 150762 + N-terminal Zn-ribbon domain and C-terminal MutT domain, YJAD ortholog (NCBI ptt file) False
CAC0333 CAC0333 CDS None chromosome 392028 394388 + Hypothetical protein, CF-7 family (NCBI ptt file) False
CAC0334 CAC0334 CDS None chromosome 394385 394885 + Hypothetical protein, CF-21 family (NCBI ptt file) False
CAC0425 sacA CDS None chromosome 491937 493409 + Sucrase-6-phosphate hydrolase (gene sacA) (NCBI ptt file) False
CAC0459 CAC0459 CDS None chromosome 529651 531534 - NtrC family transcriptional regulator (PAS and AAA domains) (NCBI ptt file) True
CAC1492 CAC1492 CDS None chromosome 1637938 1638951 + Uncharacterized protein, YhhW/pirin family (NCBI ptt file) False
CAC1589 malS CDS None chromosome 1732294 1733925 - Malic enzyme (NCBI ptt file) False
CAC1596 malS CDS None chromosome 1740023 1741654 - Malic enzyme (NCBI ptt file) False
CAC1690 pilT CDS None chromosome 1840775 1841833 + PilT ATPase involved in pili biogenesis (NCBI ptt file) False
CAC1815 recA CDS None chromosome 1965171 1966220 + RECA recombinase, ATPase (NCBI ptt file) False
CAC2549 CAC2549 CDS None chromosome 2657657 2658505 - Uncharacterized conserved protein (NCBI ptt file) False
CAC2624 dapF CDS None chromosome 2733541 2734542 - Diaminopimelate epimerase (NCBI ptt file) False
CAC2829 CAC2829 CDS None chromosome 2959977 2960516 - Predicted membrane protein (NCBI ptt file) False
CAC2830 CAC2830 CDS None chromosome 2960582 2960857 - Acylphosphatases, ACYP (NCBI ptt file) False
CAC2933 CAC2933 CDS None chromosome 3065592 3066401 - Ferredoxin-like domain fused to nitroreductase-like domain (NCBI ptt file) False
CAC3000 CAC3000 CDS None chromosome 3139107 3139490 - Hypothetical protein (NCBI ptt file) False
CAC3250 CAC3250 CDS None chromosome 3401711 3402481 - Possible glutamate racemase (NCBI ptt file) False
CAC3364 CAC3364 CDS None chromosome 3541918 3542856 - Barstar-like protein, ribonuclease (barnase) inhibitor (NCBI ptt file) False
CAC3365 CAC3365 CDS None chromosome 3542891 3543010 - Hypothetical protein (NCBI ptt file) False
CAC3366 CAC3366 CDS None chromosome 3543132 3543458 - Hypothetical protein (NCBI ptt file) False
CAC3592 CAC3592 CDS None chromosome 3794882 3795082 - Hypothetical protein, CF-27 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 92

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.