Organism : Methanococcus maripaludis S2 | Module List:
Module 27 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 27

There are 5 regulatory influences for Module 27

Regulator Table (5)
Regulator Name Type
MMP0499 tf
MMP1304 tf
MMP1447 tf
MMP0052
MMP1304
combiner
MMP0097
MMP0465
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
715 3.40e-02 GGTGat
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716 2.00e+03 TCGAGcGC.tC
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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 27 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Glycine serine and threonine metabolism kegg pathway 1.10e-05 1.27e-04 3/27
Valine leucine and isoleucine biosynthesis kegg pathway 1.00e-06 9.00e-06 4/27
Arginine and proline metabolism kegg pathway 3.60e-05 3.67e-04 3/27
Aminoacyl-tRNA biosynthesis kegg pathway 1.71e-02 3.29e-02 3/27
Metabolic pathways kegg pathway 2.00e-06 3.20e-05 15/27
Biosynthesis of secondary metabolites kegg pathway 2.80e-05 2.94e-04 8/27
Microbial metabolism in diverse environments kegg pathway 1.71e-02 3.29e-02 5/27
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 17/27
Metabolism of Cofactors and Vitamins kegg subcategory 1.92e-04 1.37e-03 5/27
Metabolism kegg subcategory 0.00e+00 0.00e+00 28/27
Metabolism kegg category 0.00e+00 0.00e+00 30/27
Global kegg category 0.00e+00 0.00e+00 28/27
Metabolism kegg category 0.00e+00 0.00e+00 19/27
Amino Acid Metabolism kegg subcategory 0.00e+00 0.00e+00 13/27
Glycine serine and threonine metabolism kegg pathway 1.10e-05 1.32e-04 3/27
Valine leucine and isoleucine biosynthesis kegg pathway 1.00e-06 9.00e-06 4/27
Arginine and proline metabolism kegg pathway 3.60e-05 3.88e-04 3/27
Metabolism of Cofactors and Vitamins kegg subcategory 1.92e-04 1.57e-03 5/27
Aminoacyl-tRNA biosynthesis kegg pathway 1.71e-02 4.21e-02 3/27
Global kegg category 4.00e-06 6.10e-05 15/27
Metabolism kegg subcategory 4.00e-06 6.10e-05 15/27
Metabolic pathways kegg pathway 2.00e-06 3.30e-05 15/27
Biosynthesis of secondary metabolites kegg pathway 2.80e-05 3.10e-04 8/27
Microbial metabolism in diverse environments kegg pathway 1.71e-02 4.21e-02 5/27

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 5.73e-03 8.73e-03 4/27
amino acid binding molecular_function 4.00e-06 1.40e-05 3/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
tRNA aminoacylation tigr sub1role 2.75e-04 1.32e-03 3/27
Protein synthesis tigr mainrole 1.53e-02 4.22e-02 3/27
Amino acid biosynthesis tigr mainrole 8.00e-06 4.20e-04 5/27
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 2.29e-03 1.49e-02 3/27
Protein synthesis tigr mainrole 1.53e-02 1.97e-02 3/27
tRNA aminoacylation tigr sub1role 2.75e-04 5.47e-04 3/27
Amino acid biosynthesis tigr mainrole 8.00e-06 2.00e-05 5/27
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 2.29e-03 3.62e-03 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 12/27
Coenzyme transport and metabolism cog subcategory 7.16e-04 9.65e-03 6/27
Metabolism cog category 1.00e-06 2.80e-05 20/27
Metabolism cog category 2.30e-05 5.30e-05 18/27
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 12/27
Coenzyme transport and metabolism cog subcategory 7.16e-04 1.27e-03 6/27
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 27

There are 27 genes in Module 27

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0003 korA CDS 2762170 chromosome 11517 12608 - 2-oxoglutarate ferredoxin oxidoreductase subunit alpha False
MMP0006 CDS 2761850 chromosome 15336 16421 + 3-dehydroquinate synthase False
MMP0073 argG CDS 2761944 chromosome 84962 86155 + argininosuccinate synthase False
MMP0103 CDS 2761393 chromosome 111821 112720 + pyridoxal biosynthesis lyase PdxS False
MMP0135 thrC CDS 2762199 chromosome 141612 142826 + threonine synthase False
MMP0136 leuD CDS 2761880 chromosome 142844 143347 + 3-isopropylmalate dehydratase small subunit False
MMP0160 ftsA-2 CDS 2762509 chromosome 169144 170445 - coenzyme F390 synthetase False
MMP0261 CDS 2762248 chromosome 261844 262134 - DNA directed RNA polymerase subunit L False
MMP0553 argF CDS 2762617 chromosome 556641 557555 - ornithine carbamoyltransferase False
MMP0654 ilvC CDS 2762719 chromosome 645729 646721 + ketol-acid reductoisomerase False
MMP0879 serS CDS 2762696 chromosome 872195 873739 - seryl-tRNA synthetase False
MMP1018 cimA CDS 2761296 chromosome 1005952 1007430 + (R)-citramalate synthase False
MMP1101 CDS 2761655 chromosome 1093257 1094444 - acetylornithine aminotransferase False
MMP1139 thiE CDS 2762052 chromosome 1128854 1129477 + thiamine-phosphate pyrophosphorylase False
MMP1149 leuC CDS 2762577 chromosome 1137792 1139066 + 3-isopropylmalate dehydratase large subunit False
MMP1196 CDS 2761778 chromosome 1183142 1183690 + hypothetical protein MMP1196 False
MMP1242 nadA CDS 2761920 chromosome 1227185 1228102 - quinolinate synthetase False
MMP1310 purO CDS 2762594 chromosome 1296054 1296659 - IMP cyclohydrolase False
MMP1311 CDS 2762046 chromosome 1296689 1296847 - ferredoxin False
MMP1497 CDS 2762497 chromosome 1458529 1459008 + hypothetical protein MMP1497 False
MMP1498 CDS 2762530 chromosome 1459005 1459787 + hypothetical protein MMP1498 False
MMP1510 gatA CDS 2761233 chromosome 1467465 1468760 - aspartyl/glutamyl-tRNA amidotransferase subunit A False
MMP1588 serA CDS 2761474 chromosome 1536504 1538075 - D-3-phosphoglycerate dehydrogenase False
MMP1592 trpS CDS 2761540 chromosome 1541201 1542277 - tryptophanyl-tRNA synthetase False
MMP1593 CDS 2761563 chromosome 1542305 1543210 - hypothetical protein MMP1593 False
MMP1701 CDS 2761360 chromosome 1642492 1642974 + amino acid-binding ACT domain-containing protein False
MMP1702 hom CDS 2762441 chromosome 1642986 1643999 + homoserine dehydrogenase 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 27

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

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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.