Organism : Methanococcus maripaludis S2 | Module List:
Module 96 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 96

There are 6 regulatory influences for Module 96

Regulator Table (6)
Regulator Name Type
MMP0052 tf
MMP1447 tf
MMP0097
MMP1052
combiner
MMP1015 tf
MMP0460 tf
MMP0052
MMP1304
combiner

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
849 1.70e+02 gAGGTGc
Loader icon
850 1.60e+04 CCcTGCc
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 96 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Ribosome kegg pathway 8.70e-05 7.61e-04 6/27
Biosynthesis of secondary metabolites kegg pathway 2.80e-02 4.67e-02 4/27
Translation kegg subcategory 9.59e-04 5.64e-03 7/27
Genetic Information Processing kegg category 9.59e-03 4.10e-02 7/27
Genetic Information Processing kegg category 6.97e-03 2.15e-02 7/27
Translation kegg subcategory 9.59e-04 5.27e-03 7/27
Ribosome kegg pathway 8.70e-05 8.12e-04 6/27

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
translation biological_process 3.00e-06 1.90e-05 7/27
protein folding biological_process 4.00e-06 2.00e-05 3/27
structural constituent of ribosome molecular_function 2.30e-05 8.30e-05 6/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 2.45e-03 1.54e-02 4/27
Protein synthesis tigr mainrole 2.45e-03 3.84e-03 4/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 3.00e-06 9.90e-05 10/27
Posttranslational modification, protein turnover, chaperones cog subcategory 5.67e-03 3.99e-02 3/27
Information storage and processing cog category 1.09e-04 1.59e-03 11/27
Information storage and processing cog category 9.20e-05 2.02e-04 11/27
Cellular processes and signaling cog category 3.03e-02 4.39e-02 5/27
Translation, ribosomal structure and biogenesis cog subcategory 3.00e-06 6.00e-06 10/27
Posttranslational modification, protein turnover, chaperones cog subcategory 5.67e-03 8.84e-03 3/27
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 96

There are 27 genes in Module 96

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0060 rplX CDS 2761240 chromosome 74160 74390 - 50S ribosomal protein LX False
MMP0061 aIF6 CDS 2761071 chromosome 74409 75092 - translation initiation factor IF-6 False
MMP0062 CDS 2761875 chromosome 75129 75380 - 50S ribosomal protein L31e False
MMP0075 CDS 2762210 chromosome 86570 87538 - abortive infection protein False
MMP0163 arsA CDS 2761519 chromosome 172067 173104 + arsenite-activated ATPase ArsA False
MMP0242 CDS 2761651 chromosome 248102 248371 - hypothetical protein MMP0242 False
MMP0245 pfdB CDS 2761940 chromosome 249805 250146 - prefoldin subunit beta False
MMP0317 CDS 2762559 chromosome 312964 314115 + hypothetical protein MMP0317 False
MMP0350 CDS 2761256 chromosome 345820 346410 + hexapeptide repeat-containing transferase False
MMP0370 CDS 2761566 chromosome 366983 368389 + hypothetical protein MMP0370 False
MMP0443 rps24e CDS 2761951 chromosome 440936 441244 + 30S ribosomal protein S24e False
MMP0572 slyD CDS 2761543 chromosome 571721 572407 - FKBP-type peptidylprolyl isomerase False
MMP0578 aroQ CDS 2761533 chromosome 575111 575401 - chorismate mutase False
MMP0657 CDS 2761090 chromosome 647675 647947 - hypothetical protein MMP0657 False
MMP0668 CDS 2762086 chromosome 657825 658433 + hypothetical protein MMP0668 False
MMP0946 gatB CDS 2761529 chromosome 933286 934695 - aspartyl/glutamyl-tRNA amidotransferase subunit B False
MMP1013 carB CDS 2761525 chromosome 998113 1001358 + carbamoyl-phosphate synthase large subunit False
MMP1113 CDS 2761746 chromosome 1103223 1104161 - transketoloase, C terminal half False
MMP1147 rpl37e CDS 2761614 chromosome 1137171 1137365 - 50S ribosomal protein L37e False
MMP1208 aIF2_gamma CDS 2761203 chromosome 1194834 1196066 + translation initiation factor IF-2 subunit gamma False
MMP1254 purM CDS 2762764 chromosome 1236961 1238010 + phosphoribosylaminoimidazole synthetase False
MMP1260 CDS 2761266 chromosome 1243648 1244796 - hypothetical protein MMP1260 False
MMP1401 ef1B CDS 2762401 chromosome 1383440 1383709 + elongation factor 1-beta False
MMP1403 rpl22p CDS 2762145 chromosome 1384030 1384491 + 50S ribosomal protein L22P False
MMP1433 rpl11p CDS 2761146 chromosome 1405125 1405604 - 50S ribosomal protein L11P False
MMP1515 hsp60 CDS 2761905 chromosome 1474553 1476184 - chaperonin GroEL False
MMP1646 CDS 2762260 chromosome 1586722 1587198 - hypothetical protein MMP1646 True

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 96

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.