Organism : Campylobacter jejuni | Module List:
Module 51 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 51

There are 0 regulatory influences for Module 51

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
7484 1.10e+04 CGAGGAC
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7485 6.80e+02 .CTcgc.g.Gg
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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 51 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Folding Sorting and Degradation kegg subcategory 2.52e-03 1.82e-02 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 3.53e-04 7.74e-04 4/30
Cations and iron carrying compounds tigr sub1role 2.00e-06 6.00e-06 4/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 1.81e-04 3.99e-04 11/30
Translation, ribosomal structure and biogenesis cog subcategory 1.98e-02 3.32e-02 5/30
Transcription cog subcategory 4.61e-03 8.23e-03 3/30
Replication, recombination and repair cog subcategory 1.72e-02 2.90e-02 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 51

There are 30 genes in Module 51

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Cj0001 dnaA CDS None chromosome 1 1323 + chromosomal replication initiator protein (NCBI ptt file) False
Cj0054c Cj0054c DUMMY None chromosome 0 0 + hypothetical protein Cj0054c (NCBI ptt file) False
Cj0181 tonB1 CDS None chromosome 177203 177949 + possible tonB transport protein (NCBI ptt file) False
Cj0183 Cj0183 DUMMY None chromosome 0 0 + putative integral membrane protein with haemolysin domain (NCBI ptt file) False
Cj0247c Cj0247c DUMMY None chromosome 0 0 + hypothetical protein Cj0247c (NCBI ptt file) False
Cj0280 Cj0280 DUMMY None chromosome 0 0 + hypothetical protein Cj0280 (NCBI ptt file) False
Cj0452 dnaQ CDS None chromosome 417629 418390 + exonuclease, possibly dna polymerase III epsilon subunit (NCBI ptt file) False
Cj0500 Cj0500 DUMMY None chromosome 0 0 + putative ATP /GTP binding protein (NCBI ptt file) False
Cj0569 Cj0569 DUMMY None chromosome 0 0 + hypothetical protein Cj0569 (NCBI ptt file) False
Cj0667 Cj0667 DUMMY None chromosome 0 0 + hypothetical protein Cj0667 (NCBI ptt file) False
Cj0712 rimM CDS None chromosome 667655 668194 + putative 16S rRNA processing protein (NCBI ptt file) False
Cj0753c tonB3 CDS None chromosome 704442 705125 - tonB transport protein (NCBI ptt file) False
Cj0831c trmA CDS None chromosome 777295 778368 - tRNA (uracil-5-)-methyltransferase (NCBI ptt file) False
Cj0886c ftsK CDS None chromosome 820683 823523 - putative cell division protein (NCBI ptt file) False
Cj0975 Cj0975 DUMMY None chromosome 0 0 + putative outer-membrane protein (NCBI ptt file) False
Cj0991c Cj0991c DUMMY None chromosome 0 0 + putative oxidoreductase ferredoxin-type electron transport protein (NCBI ptt file) False
Cj1048c dapE CDS None chromosome 980554 981651 - succinyl-diaminopimelate desuccinylase (NCBI ptt file) False
Cj1049c Cj1049c DUMMY None chromosome 0 0 + putative integral membrane protein (NCBI ptt file) False
Cj1050c Cj1050c DUMMY None chromosome 0 0 + putative transferase (NCBI ptt file) True
Cj1052c mutS CDS None chromosome 987019 989229 - putative mismatch repair protein (NCBI ptt file) False
Cj1053c Cj1053c DUMMY None chromosome 0 0 + putative integral membrane protein (NCBI ptt file) False
Cj1156 rho CDS None chromosome 1088373 1089671 + transcription termination factor (NCBI ptt file) True
Cj1161c Cj1161c DUMMY None chromosome 0 0 + putative cation-transporting ATPase (NCBI ptt file) False
Cj1163c Cj1163c DUMMY None chromosome 0 0 + putative cation transport protein (NCBI ptt file) False
Cj1206c ftsY CDS None chromosome 1135449 1136315 - putative signal recognition particle protein (NCBI ptt file) False
Cj1207c Cj1207c DUMMY None chromosome 0 0 + putative lipoprotein thiredoxin (NCBI ptt file) False
Cj1272c spoT CDS None chromosome 1204596 1206791 - putative guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase (NCBI ptt file) False
Cj1310c Cj1310c DUMMY None chromosome 0 0 + hypothetical protein Cj1310c (617 family) (NCBI ptt file) False
Cj1561 Cj1561 DUMMY None chromosome 0 0 + putative transcriptional regulator (NCBI ptt file) True
Cj1633 Cj1633 DUMMY None chromosome 0 0 + hypothetical protein Cj1633 (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 51

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.