Organism : Methanococcus maripaludis S2 | Module List:
Module 92 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 92

There are 6 regulatory influences for Module 92

Regulator Table (6)
Regulator Name Type
MMP0257 tf
MMP0907 tf
MMP0052 tf
MMP0052
MMP0257		 combiner
MMP0257
MMP1376		 combiner
MMP0568
MMP1100		 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
841 3.90e+02 ccGGtGat
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842 3.30e+03 GGCGCcAtCC
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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 92 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Pyrimidine metabolism kegg pathway 7.13e-03 1.74e-02 3/33
Ribosome kegg pathway 4.40e-05 4.38e-04 7/33
Nucleotide Metabolism kegg subcategory 4.85e-03 1.88e-02 5/33
Translation kegg subcategory 3.93e-03 1.58e-02 7/33
Genetic Information Processing kegg category 1.86e-04 1.17e-03 11/33
Pyrimidine metabolism kegg pathway 7.13e-03 2.19e-02 3/33
Genetic Information Processing kegg category 1.10e-04 9.94e-04 11/33
Translation kegg subcategory 3.93e-03 1.42e-02 7/33
Ribosome kegg pathway 4.40e-05 4.61e-04 7/33

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
translation biological_process 1.80e-05 9.10e-05 7/33
biosynthetic process biological_process 7.35e-04 1.86e-03 3/33
DNA binding molecular_function 1.17e-02 1.63e-02 3/33
structural constituent of ribosome molecular_function 1.00e-05 3.50e-05 7/33
DNA-directed DNA polymerase activity molecular_function 0.00e+00 0.00e+00 14/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Ribosomal proteins: synthesis and modification tigr sub1role 7.40e-05 6.79e-04 4/33
Protein synthesis tigr mainrole 6.08e-03 2.68e-02 4/33
Protein synthesis tigr mainrole 6.08e-03 8.72e-03 4/33
Ribosomal proteins: synthesis and modification tigr sub1role 7.40e-05 1.72e-04 4/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 2.60e-05 7.43e-04 10/33
Lipid transport and metabolism cog subcategory 1.13e-04 2.28e-03 3/33
Information storage and processing cog category 1.00e-05 1.84e-04 14/33
Information storage and processing cog category 2.07e-04 4.24e-04 12/33
Translation, ribosomal structure and biogenesis cog subcategory 2.60e-05 5.90e-05 10/33
Lipid transport and metabolism cog subcategory 1.13e-04 2.44e-04 3/33
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 92

There are 33 genes in Module 92

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0026 DP2 CDS 2762226 chromosome 33256 36651 - DNA polymerase II large subunit False
MMP0036 tfe CDS 2761565 chromosome 53793 54350 + transcription initiation factor E subunit alpha True
MMP0043 CDS 2761304 chromosome 60428 61495 + isopentenyl pyrophosphate isomerase False
MMP0099 CDS 2761945 chromosome 108126 109277 + major facilitator transporter False
MMP0134 CDS 2761806 chromosome 140997 141341 + hypothetical protein MMP0134 False
MMP0405 gch3 CDS 2762121 chromosome 404516 405316 + GTP cyclohydrolase III False
MMP0457 CDS 2761319 chromosome 450214 451830 + DEAD/DEAH box helicase domain-containing protein False
MMP0530 CDS 2761999 chromosome 535522 536139 + hypothetical protein MMP0530 False
MMP0566 CDS 2761557 chromosome 565697 567346 - AMP-binding domain-containing protein False
MMP0639 CDS 2762060 chromosome 632868 633056 - 50S ribosomal protein L24e False
MMP0640 rps28e CDS 2761066 chromosome 633076 633306 - 30S ribosomal protein S28e False
MMP0641 rpl7ae CDS 2761178 chromosome 633346 633699 - 50S ribosomal protein L7Ae False
MMP0682 CDS 2762643 chromosome 670531 671097 - hypothetical protein MMP0682 False
MMP0695 psmB CDS 2762201 chromosome 684187 684846 - proteasome subunit beta False
MMP0760 CDS 2761259 chromosome 752250 752480 - hypothetical protein MMP0760 False
MMP0943 taqD CDS 2761431 chromosome 929826 930278 - glycerol-3-phosphate cytidyltransferase False
MMP0975 modA CDS 2762274 chromosome 961541 962392 - molybdenum ABC transporter solute-binding protein False
MMP1211 CDS 2762287 chromosome 1198055 1199104 + hypothetical protein MMP1211 False
MMP1289 rpl10e CDS 2762217 chromosome 1272371 1272892 - 50S ribosomal protein L10e False
MMP1319 rps13p CDS 2762139 chromosome 1305905 1306354 + 30S ribosomal protein S13P False
MMP1361 rpoB2 CDS 2762415 chromosome 1339353 1340852 + DNA-directed RNA polymerase subunit beta'' False
MMP1379 thyA CDS 2762140 chromosome 1359094 1359732 - thymidylate synthase False
MMP1380 CDS 2761580 chromosome 1359806 1360924 + chlorohydrolase False
MMP1381 CDS 2761121 chromosome 1360985 1362253 + beta-lactamase-like protein False
MMP1396 CDS 2762156 chromosome 1376054 1377358 - aminotransferase False
MMP1400 CDS 2762400 chromosome 1383244 1383408 + hypothetical protein MMP1400 False
MMP1403 rpl22p CDS 2762145 chromosome 1384030 1384491 + 50S ribosomal protein L22P False
MMP1443 CDS 2761326 chromosome 1414018 1415142 + ATP/GTP-binding motif-containing protein False
MMP1444 CDS 2761338 chromosome 1415153 1416040 + methionine aminopeptidase False
MMP1480 CDS 2762422 chromosome 1440776 1442032 + aconitase family False
MMP1511 CDS 2761075 chromosome 1468938 1470299 - amino acid carrier protein False
MMP1543 rpl3p CDS 2762758 chromosome 1498876 1499880 + 50S ribosomal protein L3P False
MMP1710 CDS 2761381 chromosome 1647758 1648354 - hypothetical protein MMP1710 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.