Organism : Campylobacter jejuni | Module List:
Module 151 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 151

There are 3 regulatory influences for Module 151

Regulator Table (3)
Regulator Name Type
Cj0473 tf
Cj0479 tf
Cj0670 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
7684 1.10e+02 ctaa.ccTtTGgctat.gCTTttc
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7685 4.30e+03 GGcACAC
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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 151 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Oxidative phosphorylation kegg pathway 4.61e-03 2.55e-02 3/30
Lipid Metabolism kegg subcategory 8.97e-04 1.03e-02 3/30
Ribosome kegg pathway 1.52e-02 4.72e-02 3/30
Membrane Transport kegg subcategory 7.78e-03 3.38e-02 4/30
ABC transporters kegg pathway 1.34e-02 4.38e-02 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Fatty acid and phospholipid metabolism tigr mainrole 2.03e-04 4.67e-04 3/30
Biosynthesis tigr sub1role 2.03e-04 4.67e-04 3/30
Protein synthesis tigr mainrole 1.55e-03 2.93e-03 6/30
Ribosomal proteins: synthesis and modification tigr sub1role 7.07e-03 1.11e-02 3/30
Unknown function tigr mainrole 5.51e-03 8.97e-03 3/30
Enzymes of unknown specificity tigr sub1role 5.00e-05 1.26e-04 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Intracellular trafficking, secretion, and vesicular transport cog subcategory 5.51e-03 9.77e-03 3/30
Lipid transport and metabolism cog subcategory 3.12e-03 5.70e-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 151

There are 30 genes in Module 151

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Cj0081 cydA CDS None chromosome 91417 92979 + cytochrome bd oxidase subunit I (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
Cj0109 exbB3 CDS None chromosome 115702 116256 + exbB olQ family transport protein (VIMSS-AUTO) False
Cj0110 exbD3 CDS None chromosome 116265 116654 + exbD False
Cj0111 Cj0111 DUMMY None chromosome 0 0 + periplasmic protein (NCBI ptt file) False
Cj0112 Cj0112 DUMMY None chromosome 0 0 + periplasmic protein (NCBI ptt file) False
Cj0116 fabD CDS None chromosome 120763 121683 + malonyl CoA-acyl carrier protein transacylase (NCBI ptt file) False
Cj0117 pfs CDS None chromosome 121680 122369 + 5'-methylthioadenosineS-adenosylhomocysteine nucleosidase (VIMSS-AUTO) False
Cj0118 Cj0118 DUMMY None chromosome 0 0 + hypothetical protein Cj0118 (NCBI ptt file) False
Cj0119 Cj0119 DUMMY None chromosome 0 0 + hypothetical protein Cj0119 (NCBI ptt file) False
Cj0121 Cj0121 DUMMY None chromosome 0 0 + hypothetical protein Cj0121 (NCBI ptt file) False
Cj0154c Cj0154c DUMMY None chromosome 0 0 + putative methylase (NCBI ptt file) False
Cj0206 thrS CDS None chromosome 202241 204049 + threonyl-tRNA synthetase (NCBI ptt file) False
Cj0244 rpmI CDS None chromosome 226116 226307 + 50s ribosomal protein L35 (NCBI ptt file) False
Cj0245 rplT CDS None chromosome 226401 226754 + 50S ribosomal protein L20 (NCBI ptt file) False
Cj0275 clpX CDS None chromosome 251784 253037 + ATP-dependent clp protease ATP-binding subunit clpX (NCBI ptt file) False
Cj0315 Cj0315 DUMMY None chromosome 0 0 + hypothetical protein Cj0315 (NCBI ptt file) False
Cj0328c fabH CDS None chromosome 298883 299857 - 3-oxoacyl-[acyl-carrier-protein] synthase (NCBI ptt file) False
Cj0329c plsX CDS None chromosome 299850 300836 - putative fatty acidphospholipid synthesis protein (VIMSS-AUTO) False
Cj0330c rpmF CDS None chromosome 300842 300988 - 50S ribosomal protein L32 (NCBI ptt file) False
Cj0647 Cj0647 DUMMY None chromosome 0 0 + hypothetical protein Cj0647 (NCBI ptt file) False
Cj1013c Cj1013c DUMMY None chromosome 0 0 + putative membrane protein (NCBI ptt file) False
Cj1014c livF CDS None chromosome 947343 948038 - branched-chain amino-acid ABC transport system ATP-binding protein (NCBI ptt file) False
Cj1015c livG CDS None chromosome 948025 948795 - branched-chain amino-acid ABC transport system ATP-binding protein (NCBI ptt file) False
Cj1017c livH CDS None chromosome 949844 950740 - branched-chain amino-acid ABC transport system permease protein (NCBI ptt file) False
Cj1085c mfd CDS None chromosome 1015629 1018565 - transcription-repair coupling factor (NCBI ptt file) False
Cj1688c secY CDS None chromosome 1610956 1612221 - preprotein translocase subunit (NCBI ptt file) False
Cj1710c Cj1710c DUMMY None chromosome 0 0 + hypothetical protein Cj1710c (NCBI ptt file) False
Cj1711c ksgA CDS None chromosome 1623659 1624459 - putative dimethyladenosine transferase (16S rRNA dimethylase) (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.