Organism : Methanococcus maripaludis S2 | Module List:
Module 7 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 7

There are 4 regulatory influences for Module 7

Regulator Table (4)
Regulator Name Type
H2 ef
MMP0386
H2		 combiner
MMP0568
H2		 combiner
MMP0033
H2		 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
675 1.60e-01 GGTGgaA
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676 2.40e+03 cAGtTAGgTTAgTTCgAgTaGT
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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 7 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Citrate cycle (TCA cycle) kegg pathway 1.33e-04 1.08e-03 3/28
Carbon fixation pathways in prokaryotes kegg pathway 1.68e-04 1.29e-03 3/28
Valine leucine and isoleucine biosynthesis kegg pathway 2.90e-05 3.01e-04 3/28
Aminoacyl-tRNA biosynthesis kegg pathway 1.94e-02 3.58e-02 3/28
Metabolic pathways kegg pathway 1.30e-04 1.07e-03 13/28
Biosynthesis of secondary metabolites kegg pathway 1.62e-03 6.48e-03 6/28
Microbial metabolism in diverse environments kegg pathway 2.04e-02 3.71e-02 5/28
Carbohydrate Metabolism kegg subcategory 1.47e-02 4.70e-02 5/28
Nucleotide Metabolism kegg subcategory 1.09e-02 3.68e-02 4/28
Amino Acid Metabolism kegg subcategory 5.60e-05 4.71e-04 8/28
Metabolism kegg subcategory 0.00e+00 0.00e+00 24/28
Metabolism kegg category 0.00e+00 0.00e+00 24/28
Global kegg category 0.00e+00 0.00e+00 24/28
Metabolism kegg category 3.01e-04 2.14e-03 14/28
Citrate cycle (TCA cycle) kegg pathway 1.33e-04 1.16e-03 3/28
Carbon fixation pathways in prokaryotes kegg pathway 1.68e-04 1.40e-03 3/28
Nucleotide Metabolism kegg subcategory 3.35e-03 1.27e-02 4/28
Amino Acid Metabolism kegg subcategory 9.00e-06 1.09e-04 8/28
Valine leucine and isoleucine biosynthesis kegg pathway 2.90e-05 3.20e-04 3/28
Aminoacyl-tRNA biosynthesis kegg pathway 1.94e-02 4.61e-02 3/28
Global kegg category 2.24e-04 1.75e-03 13/28
Metabolism kegg subcategory 2.24e-04 1.75e-03 13/28
Metabolic pathways kegg pathway 1.30e-04 1.15e-03 13/28
Biosynthesis of secondary metabolites kegg pathway 1.62e-03 7.88e-03 6/28
Microbial metabolism in diverse environments kegg pathway 2.04e-02 4.79e-02 5/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 5.90e-05 1.54e-03 4/28
Amino acid biosynthesis tigr mainrole 1.61e-04 3.14e-03 4/28
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 5.90e-05 1.38e-04 4/28
Amino acid biosynthesis tigr mainrole 1.61e-04 3.48e-04 4/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 1.00e-06 3.90e-05 10/28
Nucleotide transport and metabolism cog subcategory 9.72e-04 1.16e-02 4/28
Metabolism cog category 0.00e+00 0.00e+00 23/28
Metabolism cog category 1.00e-05 2.20e-05 19/28
Amino acid transport and metabolism cog subcategory 1.00e-06 2.00e-06 10/28
Nucleotide transport and metabolism cog subcategory 9.72e-04 1.67e-03 4/28
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 7

There are 28 genes in Module 7

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0080 CDS 2761973 chromosome 90509 91600 + glutamate synthase large subunit False
MMP0282 purE CDS 2762126 chromosome 283401 283877 - phosphoribosylaminoimidazole carboxylase catalytic subunit False
MMP0308 CDS 2761386 chromosome 305972 306184 + SirA family protein False
MMP0318 ilvD CDS 2762188 chromosome 314207 315859 - dihydroxy-acid dehydratase False
MMP0326 metG CDS 2762723 chromosome 322398 324389 + methionyl-tRNA synthetase False
MMP0345 CDS 2761513 chromosome 341597 342424 - hypothetical protein MMP0345 False
MMP0346 CDS 2762682 chromosome 342467 343588 - 2-hydroxyglutaryl-CoA dehydratase subunit D-like protein False
MMP0359 CDS 2761116 chromosome 355921 356598 - glycosyl transferase family protein False
MMP0408 CDS 2761590 chromosome 406701 407621 + H+-transporting two-sector ATPase subunit A False
MMP0539 leuB CDS 2761734 chromosome 543913 544905 + multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase False
MMP0541 serB CDS 2762027 chromosome 545781 546422 + phosphoserine phosphatase SerB False
MMP0666 CDS 2761460 chromosome 655139 656764 - Na/Pi-cotransporter II-like protein False
MMP0696 proS CDS 2762205 chromosome 684942 686324 - prolyl-tRNA synthetase False
MMP0708 CDS 2761111 chromosome 699229 699939 + hypothetical protein MMP0708 False
MMP0893 pyrG CDS 2761197 chromosome 885559 887160 + CTP synthetase False
MMP0947 hisG CDS 2761528 chromosome 934878 935744 - ATP phosphoribosyltransferase False
MMP1018 cimA CDS 2761296 chromosome 1005952 1007430 + (R)-citramalate synthase False
MMP1105 sucC CDS 2762451 chromosome 1096371 1097459 + succinate-CoA ligase (ADP-forming), beta chain False
MMP1146 purF CDS 2761613 chromosome 1135617 1136996 - amidophosphoribosyltransferase False
MMP1266 CDS 2761205 chromosome 1250346 1251602 - glutamyl-tRNA(Gln) amidotransferase subunit D False
MMP1315 korG CDS 2761781 chromosome 1301117 1301650 - 2-oxoglutarate ferredoxin oxidoreductase subunit gamma False
MMP1316 korB CDS 2761782 chromosome 1301660 1302457 - 2-oxoglutarate ferredoxin oxidoreductase subunit beta False
MMP1352 CDS 2762463 chromosome 1331721 1332509 - ribulose-1,5-biphosphate synthetase False
MMP1470 pdfA CDS 2761294 chromosome 1430489 1430923 + prefoldin subunit alpha False
MMP1587 CDS 2762519 chromosome 1536058 1536471 - hypothetical protein MMP1587 False
MMP1588 serA CDS 2761474 chromosome 1536504 1538075 - D-3-phosphoglycerate dehydrogenase False
MMP1589 carA CDS 2761796 chromosome 1538219 1539319 + carbamoyl phosphate synthase small subunit False
MMP1615 CDS 2762486 chromosome 1561114 1561413 - hypothetical protein MMP1615 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.