Organism : Campylobacter jejuni | Module List:
Module 20 Profile

GeneModule member RegulatorRegulator MotifMotif
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 20

There are 5 regulatory influences for Module 20

Regulator Table (5)
Regulator Name Type
Cj1533c tf
Cj0368c tf
Cj1349c tf
Cj0480c tf
Cj0287c 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
7422 1.20e+03 aAAAatTTaTTTcTggGAAA
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7423 2.00e+04 TcatTCTaaCaTaaa.gcatttaA
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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 20 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 4.18e-04 6.80e-03 5/22
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 7.00e-06 5/22
Butanoate metabolism kegg pathway 0.00e+00 0.00e+00 5/22
Energy Metabolism kegg subcategory 0.00e+00 6.00e-06 9/22
Oxidative phosphorylation kegg pathway 0.00e+00 1.00e-06 7/22
Carbon fixation pathways in prokaryotes kegg pathway 0.00e+00 1.90e-05 5/22
Environmental Information Processing kegg category 2.79e-04 5.30e-03 6/22
Signal Transduction kegg subcategory 0.00e+00 1.40e-05 6/22
Two-component system kegg pathway 0.00e+00 1.40e-05 6/22
Cellular Processes kegg category 2.59e-03 1.84e-02 3/22
Cell Motility kegg subcategory 2.59e-03 1.84e-02 3/22
Biosynthesis of secondary metabolites kegg pathway 1.03e-02 3.89e-02 5/22
Microbial metabolism in diverse environments kegg pathway 4.18e-04 6.80e-03 5/22

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 5.30e-05 1.33e-04 5/22

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.50e-02 2.55e-02 11/22
Signal transduction mechanisms cog subcategory 1.56e-04 3.50e-04 4/22
Cell motility cog subcategory 2.81e-03 5.14e-03 3/22
Energy production and conversion cog subcategory 1.00e-06 3.00e-06 8/22
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 20

There are 22 genes in Module 20

Gene Member Table (22)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Cj0087 aspA CDS None chromosome 96074 97480 + aspartate ammonia-lyase (NCBI ptt file) False
Cj0408 frdC CDS None chromosome 372589 373371 + fumarate reductase cytochrome B subunit (NCBI ptt file) False
Cj0410 frdB CDS None chromosome 375339 376064 + fumarate reductase iron-sulfur protein (NCBI ptt file) False
Cj0437 sdhA CDS None chromosome 405333 407168 + succinate dehydrogenase flavoprotein subunit (NCBI ptt file) False
Cj0438 sdhB CDS None chromosome 407165 408130 + putative succinate dehydrogenase iron-sulfur protein (NCBI ptt file) False
Cj0439 sdhC CDS None chromosome 408134 408991 + putative succinate dehydrogenase subunit C (NCBI ptt file) False
Cj0459c Cj0459c DUMMY None chromosome 0 0 + hypothetical protein Cj0459c (NCBI ptt file) False
Cj1029c mapA CDS None chromosome 960835 961479 - putative lipoprotein (NCBI ptt file) False
Cj1064 Cj1064 DUMMY None chromosome 0 0 + None False
Cj1192 dctA CDS None chromosome 1119968 1121344 + putative C4-dicarboxylate transport protein (NCBI ptt file) False
Cj1222c Cj1222c DUMMY None chromosome 0 0 + putative two-component sensor (NCBI ptt file) False
Cj1225 Cj1225 DUMMY None chromosome 0 0 + hypothetical protein Cj1225 (NCBI ptt file) False
Cj1261 racR CDS None chromosome 1191788 1192459 + two-component regulator (NCBI ptt file) False
Cj1339c flaA CDS None chromosome 1269232 1270950 - flagellin (NCBI ptt file) False
Cj1357c Cj1357c DUMMY None chromosome 0 0 + putative periplasmic cytochrome C (NCBI ptt file) False
Cj1358c Cj1358c DUMMY None chromosome 0 0 + putative periplasmic cytochrome C (NCBI ptt file) False
Cj1359 ppk CDS None chromosome 1291131 1293215 + polyphosphate kinase (NCBI ptt file) False
Cj1486c Cj1486c DUMMY None chromosome 0 0 + putative periplasmic protein (NCBI ptt file) False
Cj1489c ccoO CDS None chromosome 1423577 1424242 - cb-type cytochrome C oxidase subunit II (NCBI ptt file) False
Cj1506c Cj1506c DUMMY None chromosome 0 0 + putative MCP-type signal transduction protein (NCBI ptt file) False
Cj1564 Cj1564 DUMMY None chromosome 0 0 + putative methyl-accepting chemotaxis signal transduction protein (NCBI ptt file) False
Cj1656c Cj1656c DUMMY None chromosome 0 0 + hypothetical protein Cj1656c (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.

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.