Organism : Clostridium acetobutylicum | Module List:
Module 253 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 253

There are 6 regulatory influences for Module 253

Regulator Table (6)
Regulator Name Type
CAC2934 tf
CAC0723 tf
CAC3438 tf
CAC3370 tf
CAC1226 tf
CAC2394 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
7158 1.20e-03 ggaGGag
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7159 5.40e+03 GCGCAC
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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 253 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 253

There are 27 genes in Module 253

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
CAC0013 CAC0013 CDS None chromosome 20956 21186 + Uncharacterized small conserved protein, ortholog of T.maritima (4981999) and P.abyssi (5457704) (NCBI ptt file) False
CAC0069 CAC0069 CDS None chromosome 79405 79794 + Predicted iron-binding protein, hemerythrin (NCBI ptt file) False
CAC0317 CAC0317 CDS None chromosome 370955 372451 + Sensory transduction histidine kinase (NCBI ptt file) False
CAC0481 nrdG CDS None chromosome 556583 557044 + Anaerobic ribonucleoside-triphosphate reductase activating protein, gene nrdG (NCBI ptt file) False
CAC0495 thiC CDS None chromosome 567859 568494 + Thiamine monophosphate syntase (NCBI ptt file) False
CAC0550 CAC0550 CDS None chromosome 637686 638114 + Possible sigma factor (NCBI ptt file) True
CAC0691 CAC0691 CDS None chromosome 797121 798356 + Uncharacterized conserved protein, VanW of Enterococcus faecalis related (NCBI ptt file) False
CAC0773 CAC0773 CDS None chromosome 895667 896392 + ABC-type cobalt transport protein ATPase component (NCBI ptt file) False
CAC0875 CAC0875 CDS None chromosome 1005232 1006152 + Predicted permease (NCBI ptt file) False
CAC1048 CAC1048 CDS None chromosome 1203188 1203694 + Carbonic anhydrases/acetyltransferases, isoleucine patch superfamily (NCBI ptt file) False
CAC1061 CAC1061 CDS None chromosome 1214843 1215055 + Uncharcterized protein, shares conserved domain among different RHS family proteins and WAPA of B.subtilis (NCBI ptt file) False
CAC1112 CAC1112 CDS None chromosome 1277443 1277562 - Hypothetical protein, CF-11 family (NCBI ptt file) False
CAC1117 CAC1117 CDS None chromosome 1281902 1282606 - Hypothetical protein (NCBI ptt file) False
CAC1119 CAC1119 CDS None chromosome 1283076 1283696 - Hypothetical protein (NCBI ptt file) False
CAC1174 CAC1174 CDS None chromosome 1330234 1330416 + Hypothetical protein (NCBI ptt file) False
CAC1175 CAC1175 CDS None chromosome 1330513 1330896 + Hypothetical protein, CF-35 family (NCBI ptt file) False
CAC1190 CAC1190 CDS None chromosome 1339526 1340539 + Predicted Fe-S-cluster redox enzyme, YLON B.subtilis homolog (NCBI ptt file) False
CAC1192 CAC1192 CDS None chromosome 1341163 1342632 + Phage replicative DNA helicase, YorI B.subtilis homolog (NCBI ptt file) False
CAC1193 CAC1193 CDS None chromosome 1342669 1342983 + Hypothetical protein (NCBI ptt file) False
CAC1194 CAC1194 CDS None chromosome 1342955 1343371 + Hypothetical protein (NCBI ptt file) False
CAC1209 nrdD CDS None chromosome 1353920 1356019 + Anaerobic ribonucleotide reductase (NCBI ptt file) False
CAC1519 CAC1519 CDS None chromosome 1661570 1663528 + Predicted permease (NCBI ptt file) False
CAC2369 CAC2369 CDS None chromosome 2479690 2480019 - Hypothetical protein (NCBI ptt file) False
CAC2396 CAC2396 CDS None chromosome 2505077 2505919 - Predicted xylanase/chitin deacetylase (NCBI ptt file) False
CAC2751 CAC2751 CDS None chromosome 2881274 2881777 - Predicted acetyltransferase (NCBI ptt file) False
CAC3414 CAC3414 CDS None chromosome 3598817 3600550 + ABC-type multidrug/protein/lipid transport system, ATPase component (NCBI ptt file) False
CAC3437 CAC3437 CDS None chromosome 3627534 3629159 - Predicted membrane-associated Zn-dependent protease, HtpX family (BlaR subfamily) (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 253

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.