Organism : Campylobacter jejuni | Module List:
Module 111 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 111

There are 5 regulatory influences for Module 111

Regulator Table (5)
Regulator Name Type
Cj1273c tf
Cj0473 tf
Cj0518 tf
Cj0479 tf
Cj1595 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
7604 1.20e+03 caAAGGAGA
Loader icon
7605 1.80e+04 cCCcaaTtGCTaGG
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 111 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 4.40e-05 1.69e-03 17/31
Amino sugar and nucleotide sugar metabolism kegg pathway 2.89e-04 5.40e-03 3/31
Oxidative phosphorylation kegg pathway 5.21e-03 2.76e-02 3/31
Amino Acid Metabolism kegg subcategory 6.90e-05 2.19e-03 8/31
Cysteine and methionine metabolism kegg pathway 1.07e-04 3.08e-03 3/31
Histidine metabolism kegg pathway 5.80e-05 1.96e-03 3/31
Ribosome kegg pathway 2.84e-03 1.90e-02 4/31
Global kegg category 5.30e-05 1.86e-03 16/31
Metabolism kegg subcategory 5.30e-05 1.86e-03 16/31
Metabolic pathways kegg pathway 3.80e-05 1.52e-03 16/31
Biosynthesis of secondary metabolites kegg pathway 4.47e-03 2.52e-02 7/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 4.16e-04 8.95e-04 5/31
ATP-proton motive force interconversion tigr sub1role 6.00e-06 1.50e-05 3/31
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 3.18e-03 5.58e-03 3/31
Ribosomal proteins: synthesis and modification tigr sub1role 7.97e-03 1.23e-02 3/31
Protein fate tigr mainrole 1.24e-02 1.78e-02 3/31
Amino acid biosynthesis tigr mainrole 2.62e-03 4.71e-03 4/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.14e-03 2.17e-03 17/31
Translation, ribosomal structure and biogenesis cog subcategory 2.31e-02 3.82e-02 5/31
Energy production and conversion cog subcategory 2.71e-02 4.42e-02 4/31
Nucleotide transport and metabolism cog subcategory 9.30e-03 1.62e-02 3/31
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 111

There are 31 genes in Module 111

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Cj0094 rplU CDS None chromosome 104118 104426 + 50S ribosomal protein L21 (NCBI ptt file) False
Cj0107 atpD CDS None chromosome 113912 115309 + ATP synthase F1 sector beta subunit (NCBI ptt file) False
Cj0108 atpC CDS None chromosome 115313 115702 + ATP synthase F1 sector epsilon subunit (NCBI ptt file) False
Cj0117 pfs CDS None chromosome 121680 122369 + 5'-methylthioadenosineS-adenosylhomocysteine nucleosidase (VIMSS-AUTO) False
Cj0169 sodB CDS None chromosome 166373 167035 + superoxide dismutase (Fe) (NCBI ptt file) False
Cj0245 rplT CDS None chromosome 226401 226754 + 50S ribosomal protein L20 (NCBI ptt file) False
Cj0268c Cj0268c DUMMY None chromosome 0 0 + putative transmembrane protein (NCBI ptt file) False
Cj0269c ilvE CDS None chromosome 247656 248570 - branched-chain amino acid aminotransferase (NCBI ptt file) False
Cj0511 Cj0511 DUMMY None chromosome 0 0 + putative secreted protease (NCBI ptt file) False
Cj0512 purC CDS None chromosome 479091 479801 + phosphoribosylaminoimidazole-succinocarboxamide synthase (NCBI ptt file) False
Cj0514 purQ CDS None chromosome 480057 480728 + phosphoribosylformylglycinamidine synthase I (NCBI ptt file) False
Cj0518 htpG CDS None chromosome 483003 484829 + hsp90 family heat shock protein (NCBI ptt file) True
Cj0807 Cj0807 DUMMY None chromosome 0 0 + putative oxidoreductase (NCBI ptt file) False
Cj0912c cysM CDS None chromosome 848410 849309 - cysteine synthase (NCBI ptt file) False
Cj0936 atpE CDS None chromosome 872516 872854 + ATP synthase F0 sector C subunit (NCBI ptt file) False
Cj0980 Cj0980 DUMMY None chromosome 0 0 + putative peptidase (NCBI ptt file) False
Cj0995c hemB CDS None chromosome 926169 927152 - delta-aminolevulinic acid dehydratase (NCBI ptt file) False
Cj1067 pgsA CDS None chromosome 1002567 1003103 + CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (NCBI ptt file) False
Cj1092c secF CDS None chromosome 1025265 1026236 - protein-export membrane protein (NCBI ptt file) False
Cj1094c Cj1094c DUMMY None chromosome 0 0 + putative membrane protein (NCBI ptt file) False
Cj1131c galE CDS None chromosome 1064895 1065881 - UDP-glucose 4-epimerase (NCBI ptt file) False
Cj1198 Cj1198 DUMMY None chromosome 0 0 + hypothetical protein Cj1198 (NCBI ptt file) False
Cj1365c Cj1365c DUMMY None chromosome 0 0 + putative secreted serine protease (NCBI ptt file) False
Cj1366c glmS CDS None chromosome 1300819 1302615 - glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (NCBI ptt file) False
Cj1382c fldA CDS None chromosome 1320852 1321343 - flavodoxin (NCBI ptt file) False
Cj1388 Cj1388 DUMMY None chromosome 0 0 + hypothetical protein Cj1388 (NCBI ptt file) False
Cj1407c Cj1407c DUMMY None chromosome 0 0 + putative phospho-sugar mutase (NCBI ptt file) False
Cj1479c rpsI CDS None chromosome 1414997 1415386 - 30S ribosomal protein S9 (NCBI ptt file) False
Cj1596 rplQ CDS None chromosome 1524914 1525267 + 50S ribosomal protein L17 (NCBI ptt file) False
Cj1597 hisG CDS None chromosome 1525440 1526339 + ATP phosphoribosyltransferase (NCBI ptt file) False
Cj1598 hisD CDS None chromosome 1526347 1527633 + histidinol dehydrogenase (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 111

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.