Organism : Campylobacter jejuni | Module List:
Module 109 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 109

There are 2 regulatory influences for Module 109

Regulator Table (2)
Regulator Name Type
Cj1533c tf
Cj0368c 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
7600 2.60e+04 gC..cTtTAgaAGcT.cTtGg
Loader icon
7601 2.50e+04 GaAccaTCGG
Loader icon
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 109 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.43e-02 2.45e-02 11/33
Poorly characterized cog category 2.81e-03 5.15e-03 10/33
Replication, recombination and repair cog subcategory 2.38e-02 3.92e-02 3/33
Cell wall/membrane/envelope biogenesis cog subcategory 4.80e-05 1.16e-04 9/33
Carbohydrate transport and metabolism cog subcategory 1.72e-03 3.21e-03 4/33
General function prediction only cog subcategory 9.80e-04 1.87e-03 8/33
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 109

There are 33 genes in Module 109

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Cj0225 Cj0225 DUMMY None chromosome 0 0 + putative acetyltransferase (NCBI ptt file) False
Cj0349 trpA CDS None chromosome 320000 320749 + tryptophan synthase alpha chain (NCBI ptt file) False
Cj0353c Cj0353c DUMMY None chromosome 0 0 + phosphatase (NCBI ptt file) False
Cj0633 Cj0633 DUMMY None chromosome 0 0 + putative periplasmic protein (NCBI ptt file) False
Cj0634 Cj0634 DUMMY None chromosome 0 0 + SMF family protein (NCBI ptt file) False
Cj0635 Cj0635 DUMMY None chromosome 0 0 + hypothetical protein Cj0635 (NCBI ptt file) False
Cj0652 pbpC CDS None chromosome 611298 613103 + penicillin-binding protein (NCBI ptt file) False
Cj0985c hipO CDS None chromosome 918580 919731 - hippurate hydrolase (NCBI ptt file) False
Cj1081c thiE CDS None chromosome 1012752 1013384 - thiamin-phosphate pyrophosphorylase (NCBI ptt file) False
Cj1109 aat CDS None chromosome 1042554 1043201 + putative leucyl/phenylalanyl-tRNA--protein transferase (NCBI ptt file) False
Cj1122c wlaJ CDS None chromosome 1055060 1055713 - putative integral membrane protein (NCBI ptt file) False
Cj1123c wlaI CDS None chromosome 1055670 1056257 - putative transferase (NCBI ptt file) False
Cj1124c wlaH CDS None chromosome 1056244 1056846 - putative galactosyltransferase (NCBI ptt file) False
Cj1125c wlaG CDS None chromosome 1056839 1057969 - putative galactosyltransferase (NCBI ptt file) False
Cj1127c wlaE CDS None chromosome 1060124 1061221 - putative glycosyltransferase (NCBI ptt file) False
Cj1174 Cj1174 DUMMY None chromosome 0 0 + putative efflux protein (NCBI ptt file) False
Cj1319 Cj1319 DUMMY None chromosome 0 0 + putative nucleotide sugar dehydratase (NCBI ptt file) False
Cj1330 Cj1330 DUMMY None chromosome 0 0 + hypothetical protein Cj1330 (NCBI ptt file) False
Cj1333 Cj1333 DUMMY None chromosome 0 0 + hypothetical protein Cj1333 (1318 family) (NCBI ptt file) False
Cj1415c cysC CDS None chromosome 1348349 1348861 - possible adenylylsulfate kinase (NCBI ptt file) False
Cj1417c Cj1417c DUMMY None chromosome 0 0 + hypothetical protein Cj1417c (NCBI ptt file) False
Cj1418c Cj1418c DUMMY None chromosome 0 0 + hypothtical protein Cj1418c (NCBI ptt file) False
Cj1423c Cj1423c DUMMY None chromosome 0 0 + putative sugar-phosphate nucleotidyltransferase (NCBI ptt file) False
Cj1424c gmhA2 CDS None chromosome 1358689 1359294 - putative phosphoheptose isomerase (NCBI ptt file) False
Cj1425c Cj1425c DUMMY None chromosome 0 0 + putative sugar kinase (NCBI ptt file) False
Cj1427c Cj1427c DUMMY None chromosome 0 0 + putative sugar-nucleotide epimerase/dehydratease (NCBI ptt file) False
Cj1428c fcl CDS None chromosome 1362156 1363196 - putative fucose synthetase (NCBI ptt file) False
Cj1429c Cj1429c DUMMY None chromosome 0 0 + hypothetical protein Cj1429c (NCBI ptt file) False
Cj1432c Cj1432c DUMMY None chromosome 0 0 + putative sugar transferase (NCBI ptt file) False
Cj1443c kpsF CDS None chromosome 1382528 1383475 - KpsF protein (NCBI ptt file) False
Cj1533c Cj1533c DUMMY None chromosome 0 0 + putative helix-turn-helix containsing protein (NCBI ptt file) True
Cj1601 hisA CDS None chromosome 1529269 1530000 + phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI ptt file) False
Cj1620c mutY CDS None chromosome 1547741 1548760 - A/G-specific adenine glycosylase (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 109

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.