Organism : Methanococcus maripaludis S2 | Module List:
Module 19 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 19

There are 4 regulatory influences for Module 19

Regulator Table (4)
Regulator Name Type
MMP1100 tf
MMP0052
Formate
combiner
MMP0097
Formate
combiner
MMP0018
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
699 7.40e+01 TaTaTaaa.tTTtctAtTtga.tt
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700 1.10e+04 GCCGGA
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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 19 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Methane metabolism kegg pathway 0.00e+00 2.00e-06 12/32
Metabolic pathways kegg pathway 1.88e-04 1.41e-03 14/32
Microbial metabolism in diverse environments kegg pathway 0.00e+00 1.00e-06 13/32
Energy Metabolism kegg subcategory 0.00e+00 1.00e-06 14/32
Metabolism kegg subcategory 0.00e+00 0.00e+00 29/32
Metabolism kegg category 1.05e-02 4.39e-02 17/32
Global kegg category 0.00e+00 0.00e+00 29/32
Metabolism kegg category 1.84e-03 8.50e-03 14/32
Energy Metabolism kegg subcategory 0.00e+00 2.00e-06 13/32
Methane metabolism kegg pathway 0.00e+00 2.00e-06 12/32
Global kegg category 3.30e-04 2.31e-03 14/32
Metabolism kegg subcategory 3.30e-04 2.31e-03 14/32
Metabolic pathways kegg pathway 1.88e-04 1.54e-03 14/32
Microbial metabolism in diverse environments kegg pathway 0.00e+00 1.00e-06 13/32

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
methanogenesis biological_process 0.00e+00 0.00e+00 5/32
catalytic activity molecular_function 2.60e-02 3.29e-02 3/32
electron carrier activity molecular_function 3.65e-03 6.04e-03 4/32
formylmethanofuran dehydrogenase activity molecular_function 0.00e+00 0.00e+00 5/32
coenzyme-B sulfoethylthiotransferase activity molecular_function 0.00e+00 0.00e+00 3/32
iron-sulfur cluster binding molecular_function 1.14e-02 1.58e-02 4/32

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Methanogenesis tigr sub1role 0.00e+00 4.00e-06 6/32
Energy metabolism tigr mainrole 6.00e-06 3.50e-04 7/32
Energy metabolism tigr mainrole 6.00e-06 1.40e-05 7/32
Methanogenesis tigr sub1role 0.00e+00 1.00e-06 6/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Coenzyme transport and metabolism cog subcategory 2.12e-03 1.92e-02 6/32
Energy production and conversion cog subcategory 1.40e-02 2.11e-02 6/32
Coenzyme transport and metabolism cog subcategory 2.12e-03 3.42e-03 6/32
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 19

There are 32 genes in Module 19

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Antisense_27 novel None chromosome 1577481 1578851 - None False
MMP0041 tfb CDS 2761541 chromosome 58605 59624 - transcription initiation factor IIB True
MMP0042 CDS 2762735 chromosome 59643 59924 - H/ACA RNA-protein complex component Gar1 False
MMP0278 CDS 2762173 chromosome 279585 280046 + putative CBS domain-containing signal transduction protein False
MMP0344 CDS 2762558 chromosome 340591 341472 - hypothetical protein MMP0344 False
MMP0405 gch3 CDS 2762121 chromosome 404516 405316 + GTP cyclohydrolase III False
MMP0407 CDS 2762031 chromosome 406129 406542 - hypothetical protein MMP0407 False
MMP0632 CDS 2761592 chromosome 624435 625601 + ATP/GTP-binding motif-containing protein False
MMP0736 CDS 2761087 chromosome 729123 729377 + PRC-barrel domain-containing protein False
MMP0762 CDS 2761288 chromosome 753135 753662 + hypothetical protein MMP0762 False
MMP1067 CDS 2762543 chromosome 1058824 1060308 - succinate dehydrogenase/fumarate reductase iron-sulfur subunit False
MMP1223 CDS 2762267 chromosome 1211914 1213392 - hypothetical protein MMP1223 False
MMP1244 fwdH CDS 2761637 chromosome 1228973 1229419 + tungsten containing formylmethanofuran dehydrogenase subunit H False
MMP1245 fwdF CDS 2761730 chromosome 1229443 1230501 + tungsten containing formylmethanofuran dehydrogenase subunit F False
MMP1246 fwdG CDS 2762563 chromosome 1230524 1230766 + tungsten containing formylmethanofuran dehydrogenase subunit G False
MMP1247 fwdD CDS 2762789 chromosome 1230808 1231194 + tungsten containing formylmethanofuran dehydrogenase subunit D False
MMP1248 fwdA CDS 2762779 chromosome 1231217 1232920 + tungsten containing formylmethanofuran dehydrogenase subunit A False
MMP1249 fwdC CDS 2762780 chromosome 1232954 1233772 + tungsten containing formylmethanofuran dehydrogenase subunit C False
MMP1257 CDS 2762607 chromosome 1240285 1240962 - NERD domain-containing protein False
MMP1258 hemB CDS 2762619 chromosome 1240981 1241949 - delta-aminolevulinic acid dehydratase False
MMP1475 CDS 2761708 chromosome 1436584 1437417 - hypothetical protein MMP1475 False
MMP1511 CDS 2761075 chromosome 1468938 1470299 - amino acid carrier protein False
MMP1555 mcrB CDS 2761737 chromosome 1509697 1511028 + methyl-coenzyme M reductase I subunit beta False
MMP1556 mcrD CDS 2762596 chromosome 1511040 1511519 + methyl-coenzyme M reductase I, protein D False
MMP1557 mcrC CDS 2762597 chromosome 1511528 1512124 + methyl coenzyme M reductase I, protein C False
MMP1558 mcrG CDS 2762397 chromosome 1512134 1512916 + methyl-coenzyme M reductase I subunit gamma False
MMP1559 mcrA CDS 2761113 chromosome 1512964 1514625 + methyl-coenzyme M reductase I subunit alpha False
MMP1586 CDS 2762392 chromosome 1535794 1536036 + hypothetical protein MMP1586 False
MMP1609 ftr CDS 2762484 chromosome 1556252 1557160 + formylmethanofuran--tetrahydromethanopterin formyltransferase False
MMP1610 CDS 2762492 chromosome 1557230 1557904 + hypothetical protein MMP1610 False
MMP1637 CDS 2762518 chromosome 1578917 1579609 - hypothetical protein MMP1637 False
MMP1712 CDS 2762365 chromosome 1649205 1650095 - LysR family transcriptional regulator True

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 19

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.