Organism : Methanococcus maripaludis S2 | Module List:
Module 40 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 40

There are 4 regulatory influences for Module 40

Regulator Table (4)
Regulator Name Type
MMP0907
H2		 combiner
MMP0386
MMP0629		 combiner
MMP0629
MMP0907		 combiner
MMP1275
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
741 3.30e-03 AatTCACCa.
Loader icon
742 4.00e+04 CCccaGAGG
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 40 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 1.14e-03 5.01e-03 10/23
Biosynthesis of secondary metabolites kegg pathway 2.80e-03 9.52e-03 5/23
Amino Acid Metabolism kegg subcategory 7.90e-05 6.48e-04 7/23
Replication and Repair kegg subcategory 9.00e-06 9.70e-05 4/23
Metabolism kegg subcategory 1.00e-05 1.00e-04 17/23
Metabolism kegg category 7.07e-04 3.99e-03 15/23
Global kegg category 1.00e-05 7.20e-05 17/23
Metabolism kegg category 1.68e-03 8.08e-03 11/23
Carbohydrate Metabolism kegg subcategory 1.33e-02 3.50e-02 3/23
Amino Acid Metabolism kegg subcategory 1.09e-03 5.81e-03 5/23
Global kegg category 1.73e-03 8.17e-03 10/23
Metabolism kegg subcategory 1.73e-03 8.17e-03 10/23
Metabolic pathways kegg pathway 1.14e-03 6.00e-03 10/23
Biosynthesis of secondary metabolites kegg pathway 2.80e-03 1.14e-02 5/23

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 5.90e-05 1.54e-03 4/23
Amino acid biosynthesis tigr mainrole 5.90e-05 1.39e-04 4/23

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 2.63e-03 2.21e-02 3/23
Amino acid transport and metabolism cog subcategory 8.50e-05 1.80e-03 7/23
Metabolism cog category 4.13e-03 3.77e-02 13/23
Metabolism cog category 8.86e-03 1.36e-02 12/23
Carbohydrate transport and metabolism cog subcategory 2.63e-03 4.21e-03 3/23
Amino acid transport and metabolism cog subcategory 8.50e-05 1.87e-04 7/23
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 40

There are 23 genes in Module 40

Gene Member Table (23)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0098 CDS 2761685 chromosome 107786 107983 - ferredoxin False
MMP0230 CDS 2761982 chromosome 238779 239465 - metal dependent phosphohydrolase False
MMP0318 ilvD CDS 2762188 chromosome 314207 315859 - dihydroxy-acid dehydratase False
MMP0326 metG CDS 2762723 chromosome 322398 324389 + methionyl-tRNA synthetase False
MMP0393 CDS 2761448 chromosome 391261 391776 - phosphodiesterase False
MMP0408 CDS 2761590 chromosome 406701 407621 + H+-transporting two-sector ATPase subunit A False
MMP0541 serB CDS 2762027 chromosome 545781 546422 + phosphoserine phosphatase SerB False
MMP0583 CDS 2761080 chromosome 578668 578976 + branched chain amino acid ABC transporter False
MMP0708 CDS 2761111 chromosome 699229 699939 + hypothetical protein MMP0708 False
MMP0872 hemC CDS 2762513 chromosome 863940 864854 + porphobilinogen deaminase False
MMP0887 CDS 2761538 chromosome 880212 880514 - stress responsive alpha-beta barrel domain-containing protein False
MMP0947 hisG CDS 2761528 chromosome 934878 935744 - ATP phosphoribosyltransferase False
MMP1032 rpa CDS 2761413 chromosome 1023461 1025389 - replication factor A False
MMP1075 dut CDS 2761784 chromosome 1065449 1065919 - dUTP diphosphatase False
MMP1076 CDS 2761822 chromosome 1065921 1067156 - hexapeptide repeat-containing transferase False
MMP1077 CDS 2762645 chromosome 1067165 1068508 - phosphoglucomutase/phosphomannomutase False
MMP1116 CDS 2761521 chromosome 1106057 1107109 + cellulase False
MMP1129 ppiB CDS 2762628 chromosome 1119759 1120247 - cyclophilin type peptidyl-prolyl cis-trans isomerase False
MMP1205 aroA CDS 2761037 chromosome 1191279 1192568 - 3-phosphoshikimate 1-carboxyvinyltransferase False
MMP1260 CDS 2761266 chromosome 1243648 1244796 - hypothetical protein MMP1260 False
MMP1266 CDS 2761205 chromosome 1250346 1251602 - glutamyl-tRNA(Gln) amidotransferase subunit D 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.

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.