Organism : Campylobacter jejuni | Module List:
Module 26 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 26

There are 0 regulatory influences for Module 26

Warning: No Regulators were found!

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
7434 2.10e+00 atttttAAGGAAAAa
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7435 8.20e+02 GCCCTAGCC
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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 26 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Replication and Repair kegg subcategory 3.12e-03 2.00e-02 3/30
Mismatch repair kegg pathway 9.40e-05 2.74e-03 3/30

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 26

There are 30 genes in Module 26

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Cj0053c trmU CDS None chromosome 68532 69548 - tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI ptt file) False
Cj0101 Cj0101 DUMMY None chromosome 0 0 + parB family protein (NCBI ptt file) True
Cj0251c Cj0251c DUMMY None chromosome 0 0 + highly acidic protein (NCBI ptt file) False
Cj0273 fabZ CDS None chromosome 250590 251030 + (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase (NCBI ptt file) False
Cj0295 Cj0295 DUMMY None chromosome 0 0 + putative acetyltransferase (NCBI ptt file) False
Cj0443 accA CDS None chromosome 411269 412207 + acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha (NCBI ptt file) False
Cj0540 Cj0540 DUMMY None chromosome 0 0 + hypothetical protein Cj0540 (NCBI ptt file) False
Cj0586 ligA CDS None chromosome 545332 547275 + DNA ligase (NCBI ptt file) False
Cj0672 Cj0672 DUMMY None chromosome 0 0 + putative periplasmic protein (NCBI ptt file) False
Cj0777 Cj0777 DUMMY None chromosome 0 0 + putative ATP-dependent DNA helicase (NCBI ptt file) False
Cj0884 rpsO CDS None chromosome 820325 820597 + 30S ribosomal protein S15 (NCBI ptt file) False
Cj0886c ftsK CDS None chromosome 820683 823523 - putative cell division protein (NCBI ptt file) False
Cj0906c Cj0906c DUMMY None chromosome 0 0 + putative periplasmic protein (NCBI ptt file) False
Cj0954c Cj0954c DUMMY None chromosome 0 0 + putative dnaJ-like protein (NCBI ptt file) False
Cj0955c purL CDS None chromosome 894780 896966 - phosphoribosylformylglycinamidine synthase (NCBI ptt file) False
Cj0958c Cj0958c DUMMY None chromosome 0 0 + putative membrane protein (NCBI ptt file) False
Cj0981c Cj0981c DUMMY None chromosome 0 0 + transmembrane transport protein (NCBI ptt file) False
Cj0986c Cj0986c DUMMY None chromosome 0 0 + putative integral membrane protein (NCBI ptt file) False
Cj1057c Cj1057c DUMMY None chromosome 0 0 + putative coiled-coil protein (NCBI ptt file) False
Cj1180c Cj1180c DUMMY None chromosome 0 0 + putative ABC transporter ATP binding protein (NCBI ptt file) False
Cj1194 Cj1194 DUMMY None chromosome 0 0 + possible phosphate permease (NCBI ptt file) False
Cj1210 Cj1210 DUMMY None chromosome 0 0 + putative integral membrane protein (NCBI ptt file) False
Cj1216c Cj1216c DUMMY None chromosome 0 0 + hypothetical protein Cj1216c (NCBI ptt file) False
Cj1217c Cj1217c DUMMY None chromosome 0 0 + hypothetical protein Cj1217c (NCBI ptt file) False
Cj1256c Cj1256c DUMMY None chromosome 0 0 + putative membrane protein (NCBI ptt file) False
Cj1282 mrdB CDS None chromosome 1213903 1215003 + RodA protein homolog (NCBI ptt file) False
Cj1437c Cj1437c DUMMY None chromosome 0 0 + putative aminotransferase (NCBI ptt file) False
Cj1483c Cj1483c DUMMY None chromosome 0 0 + putative lipoprotein (NCBI ptt file) False
Cj1567c nuoM CDS None chromosome 1497800 1499287 - NADH dehydrogenase I chain M (NCBI ptt file) False
Cj1675 fliQ CDS None chromosome 1595774 1596043 + flagellar biosynthetic protein (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.