Organism : Methanococcus maripaludis S2 | Module List:
Module 10 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 10

There are 0 regulatory influences for Module 10

Warning: No Regulators were found!

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
681 4.20e-03 cTAtTTATCATgATtgATAATtA
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682 1.20e+03 CTAACGGTGc
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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 10 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Glycolysis / Gluconeogenesis kegg pathway 1.00e-06 8.00e-06 5/25
Citrate cycle (TCA cycle) kegg pathway 3.00e-06 3.90e-05 4/25
Pyruvate metabolism kegg pathway 0.00e+00 1.00e-06 5/25
Propanoate metabolism kegg pathway 0.00e+00 0.00e+00 5/25
Butanoate metabolism kegg pathway 0.00e+00 2.00e-06 4/25
Carbon fixation pathways in prokaryotes kegg pathway 0.00e+00 2.00e-06 5/25
Methane metabolism kegg pathway 0.00e+00 0.00e+00 20/25
Valine leucine and isoleucine degradation kegg pathway 0.00e+00 3.00e-06 3/25
Nitrotoluene degradation kegg pathway 0.00e+00 0.00e+00 8/25
Metabolic pathways kegg pathway 2.80e-02 4.67e-02 8/25
Microbial metabolism in diverse environments kegg pathway 9.00e-06 1.07e-04 9/25
Carbohydrate Metabolism kegg subcategory 0.00e+00 0.00e+00 23/25
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 25/25
Xenobiotics Biodegradation and Metabolism kegg subcategory 0.00e+00 0.00e+00 8/25
Metabolism kegg subcategory 1.10e-05 1.16e-04 18/25
Metabolism kegg category 0.00e+00 0.00e+00 59/25
Global kegg category 1.10e-05 8.20e-05 18/25
Metabolism kegg category 0.00e+00 0.00e+00 23/25
Carbohydrate Metabolism kegg subcategory 3.92e-04 2.58e-03 5/25
Glycolysis / Gluconeogenesis kegg pathway 1.00e-06 9.00e-06 5/25
Citrate cycle (TCA cycle) kegg pathway 3.00e-06 4.00e-05 4/25
Pyruvate metabolism kegg pathway 0.00e+00 1.00e-06 5/25
Propanoate metabolism kegg pathway 0.00e+00 0.00e+00 5/25
Butanoate metabolism kegg pathway 0.00e+00 2.00e-06 4/25
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 20/25
Carbon fixation pathways in prokaryotes kegg pathway 0.00e+00 2.00e-06 5/25
Methane metabolism kegg pathway 0.00e+00 0.00e+00 20/25
Valine leucine and isoleucine degradation kegg pathway 0.00e+00 4.00e-06 3/25
Xenobiotics Biodegradation and Metabolism kegg subcategory 0.00e+00 0.00e+00 8/25
Nitrotoluene degradation kegg pathway 0.00e+00 0.00e+00 8/25
Global kegg category 2.29e-04 1.75e-03 12/25
Metabolism kegg subcategory 2.29e-04 1.75e-03 12/25
Microbial metabolism in diverse environments kegg pathway 9.00e-06 1.11e-04 9/25

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 0.00e+00 0.00e+00 13/25
metabolic process biological_process 2.25e-02 2.78e-02 3/25
NADH dehydrogenase (ubiquinone) activity molecular_function 0.00e+00 1.00e-06 4/25
electron carrier activity molecular_function 1.00e-06 3.00e-06 7/25
pyruvate synthase activity molecular_function 0.00e+00 0.00e+00 4/25
iron-sulfur cluster binding molecular_function 6.00e-05 2.15e-04 6/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 15/25
Inorganic ion transport and metabolism cog subcategory 3.17e-03 2.60e-02 4/25
Metabolism cog category 0.00e+00 4.00e-06 20/25
Metabolism cog category 0.00e+00 1.00e-06 19/25
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 15/25
Inorganic ion transport and metabolism cog subcategory 3.17e-03 5.04e-03 4/25
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 10

There are 25 genes in Module 10

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0984 cdh CDS 2761647 chromosome 969513 970031 - acetyl-CoA decarbonylase/synthase complex subunit epsilon False
MMP0985 cdhA CDS 2761656 chromosome 970041 972377 - acetyl-CoA decarbonylase/synthase complex subunit alpha False
MMP1152 CDS 2762038 chromosome 1141022 1141384 - hypothetical protein MMP1152 False
MMP1153 ehbN CDS 2762039 chromosome 1141444 1142571 - energy conserving hydrogenase B large subunit False
MMP1271 vorA CDS 2761774 chromosome 1255312 1256751 - 2-oxoisovalerate oxidoreductase subunit alpha False
MMP1272 vorB CDS 2761775 chromosome 1256753 1257808 - 2-ketoisovalerate ferredoxin reductase False
MMP1273 vorC CDS 2762243 chromosome 1257819 1258058 - 2-oxoisovalerate oxidoreductase subunit gamma False
MMP1274 CDS 2761799 chromosome 1258142 1259815 - AMP-dependent synthetase and ligase False
MMP1275 CDS 2761800 chromosome 1259867 1260421 - hypothetical protein MMP1275 True
MMP1469 ehbA CDS 2761293 chromosome 1429995 1430297 - putative monovalent cation/H+ antiporter subunit E False
MMP1502 porF CDS 2762698 chromosome 1462535 1462951 - hypothetical protein MMP1502 False
MMP1503 porE CDS 2762699 chromosome 1462970 1463473 - pyruvate oxidoreductase-associated False
MMP1504 porB CDS 2762023 chromosome 1463497 1464393 - pyruvate ferredoxin oxidoreductase subunit beta False
MMP1505 porA CDS 2761618 chromosome 1464410 1465573 - pyruvate oxidoreductase (synthase) subunit alpha False
MMP1506 porD CDS 2761619 chromosome 1465595 1465852 - pyruvate oxidoreductase (synthase) subunit delta False
MMP1507 porC CDS 2761084 chromosome 1465867 1466397 - pyruvate ferredoxin oxidoreductase subunit gamma False
MMP1621 ehbO CDS 2761291 chromosome 1565956 1566951 - energy conserving hydrogenase B integral membrane subunit False
MMP1622 ehbM CDS 2761623 chromosome 1566962 1567405 - energy conserving hydrogenase B small subunit False
MMP1623 ehbL CDS 2762013 chromosome 1567415 1567927 - ferredoxin False
MMP1624 ehbK CDS 2762791 chromosome 1567947 1569392 - polyferredoxin False
MMP1625 ehbJ CDS 2762539 chromosome 1569394 1569654 - hypothetical protein MMP1625 False
MMP1626 CDS 2761653 chromosome 1569666 1570427 - putative monovalent cation/H+ antiporter subunit B False
MMP1627 ehbG CDS 2762655 chromosome 1570437 1570745 - hypothetical protein MMP1627 False
MMP1628 ehbF CDS 2761605 chromosome 1570763 1572211 - hydrogenase subunit F False
MMP1629 ehbE CDS 2761620 chromosome 1572237 1572593 - putative monovalent cation/H+ antiporter subunit C 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 10

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.