Organism : Clostridium acetobutylicum | Module List:
Module 4 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 4

There are 7 regulatory influences for Module 4

Regulator Table (7)
Regulator Name Type
CAC3166 tf
CAC0627 tf
CAC3438 tf
CAC3409 tf
CAC2552 tf
CAC3236 tf
CAC1770 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
6662 3.70e-06 tagGAGGa
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6663 4.40e+02 ACAGGaTGG
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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 4 is enriched for following functions.

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 4

There are 34 genes in Module 4

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0263 serB CDS None chromosome 295415 296158 + Phosphoserine phosphatase related protein (NCBI ptt file) False
CAC0309 CAC0309 CDS None chromosome 362633 363748 + Cell wall-associated hydrolase (NCBI ptt file) False
CAC0312 CAC0312 CDS None chromosome 366191 366847 - Hypothetical protein (NCBI ptt file) False
CAC0313 CAC0313 CDS None chromosome 366858 367514 - Phage shock protein A (NCBI ptt file) False
CAC0538 CAC0538 CDS None chromosome 624572 626167 + Beta-mannanase ManB-like enzyme, contains ChW-repeats (NCBI ptt file) False
CAC0697 CAC0697 CDS None chromosome 806192 807214 + Galactose mutarotase related enzyme (NCBI ptt file) False
CAC0722 CAC0722 CDS None chromosome 837343 837879 - Predicted membrane protein; CF-9 family (NCBI ptt file) False
CAC1048 CAC1048 CDS None chromosome 1203188 1203694 + Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily (NCBI ptt file) False
CAC1139 CAC1139 CDS None chromosome 1304361 1306796 - Phage related protein, YonO B.subtilis homolog (NCBI ptt file) False
CAC1165 CAC1165 CDS None chromosome 1324373 1324621 + Hypothetical protein (NCBI ptt file) False
CAC1184 CAC1184 CDS None chromosome 1335325 1335606 + Hypothetical protein (NCBI ptt file) False
CAC1215 CAC1215 CDS None chromosome 1359858 1360031 + Hypothetical protein (NCBI ptt file) False
CAC1319 glpF CDS None chromosome 1460057 1460758 + Glycerol uptake facilitator protein, GLPF (NCBI ptt file) False
CAC1320 glpP CDS None chromosome 1460835 1461392 + Glycerol-3-phosphate responsive antiterminator (mRNA-binding), GLPP (NCBI ptt file) True
CAC1464 CAC1464 CDS None chromosome 1613639 1615906 + UVRA-like protein, probably involved in MDR transport (NCBI ptt file) False
CAC1606 CAC1606 CDS None chromosome 1749316 1750047 - Uncharacterized conserved protein (NCBI ptt file) False
CAC1607 CAC1607 CDS None chromosome 1750067 1750342 - Hypothetical protein (NCBI ptt file) False
CAC2050 CAC2050 CDS None chromosome 2158065 2158397 - Predicted membrane protein (NCBI ptt file) False
CAC2257 CAC2257 CDS None chromosome 2357241 2358098 + Hypothetical protein (NCBI ptt file) False
CAC2322 CAC2322 CDS None chromosome 2424144 2424407 + Hypothetical protein (NCBI ptt file) False
CAC2504 CAC2504 CDS None chromosome 2612211 2612447 - Hypothetical protein (NCBI ptt file) False
CAC2689 CAC2689 CDS None chromosome 2812375 2812908 + Uncharacterized protein, YJCM B.subtilis ortholog (NCBI ptt file) False
CAC2992 CAC2992 CDS None chromosome 3129917 3130705 - Predicted short-chain dehydrogenase (NCBI ptt file) False
CAC3087 CAC3087 CDS None chromosome 3239451 3241070 - Phosphoenolpyruvate-protein kinase (PTS system enzyme I) (NCBI ptt file) False
CAC3264 CAC3264 CDS None chromosome 3414170 3414571 - Uncharacterized conserved protein, YTFJ B.subtilis ortholog (NCBI ptt file) False
CAC3280 CAC3280 CDS None chromosome 3437236 3439785 + Possible surface protein, responsible for cell interaction; contains cell adhesion domain and ChW-repeats (NCBI ptt file) False
CAC3341 CAC3341 CDS None chromosome 3514066 3514692 + Multimeric flavodoxin WrbA family protein (NCBI ptt file) False
CAC3346 CAC3346 CDS None chromosome 3518656 3520074 + MDR-type permease (NCBI ptt file) False
CAC3430 CAC3430 CDS None chromosome 3617114 3618307 - Membrane associated, signal transduction histidine kinase-like ATPase (NCBI ptt file) False
CAC3548 CAC3548 CDS None chromosome 3744073 3744264 - Uncharacterized conserved Zn-finger containing protein (NCBI ptt file) False
CAC3597 CAC3597 CDS None chromosome 3800115 3800660 - Rubrerythrin (NCBI ptt file) False
CAC3598 CAC3598 CDS None chromosome 3800735 3801280 - Rubrerythrin (NCBI ptt file) False
CAC3599 CAC3599 CDS None chromosome 3801709 3801900 + Hypothetical protein (NCBI ptt file) False
CAC3623 CAC3623 CDS None chromosome 3825258 3826028 + Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) (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 4

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.