Organism : Methanococcus maripaludis S2 | Module List:
Module 9 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 9

There are 3 regulatory influences for Module 9

Regulator Table (3)
Regulator Name Type
H2 ef
MMP0629 tf
MMP1100 tf

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
679 2.10e-01 TGaCtGATTAaTCAA
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680 5.20e+00 gGttaTgtgggtagcAc
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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 9 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Glyoxylate and dicarboxylate metabolism kegg pathway 0.00e+00 0.00e+00 4/28
Methane metabolism kegg pathway 1.60e-05 1.72e-04 9/28
Microbial metabolism in diverse environments kegg pathway 1.92e-04 1.44e-03 8/28
Energy Metabolism kegg subcategory 3.40e-05 3.04e-04 10/28
Metabolism kegg subcategory 2.21e-03 1.02e-02 16/28
Global kegg category 2.21e-03 1.10e-02 16/28
Carbohydrate Metabolism kegg subcategory 4.99e-03 1.67e-02 4/28
Glyoxylate and dicarboxylate metabolism kegg pathway 0.00e+00 0.00e+00 4/28
Energy Metabolism kegg subcategory 1.10e-05 1.33e-04 10/28
Methane metabolism kegg pathway 1.60e-05 1.81e-04 9/28
Microbial metabolism in diverse environments kegg pathway 1.92e-04 1.57e-03 8/28

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 1.53e-03 3.18e-03 6/28
formate dehydrogenase (NAD+) activity molecular_function 0.00e+00 0.00e+00 4/28
electron carrier activity molecular_function 1.98e-03 3.60e-03 4/28
iron-sulfur cluster binding molecular_function 1.34e-04 4.25e-04 6/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 2.71e-04 4.53e-03 8/28
Energy production and conversion cog subcategory 2.71e-04 5.36e-04 8/28
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 9

There are 28 genes in Module 9

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Antisense_22 novel None chromosome 1282479 1282555 - None False
MMP0057 cofH CDS 2762565 chromosome 71296 72372 - FO synthase subunit 2 False
MMP0138 fdhA CDS 2762026 chromosome 145038 147068 + formate dehydrogenase subunit alpha False
MMP0139 fdhB CDS 2762396 chromosome 147092 148219 + formate dehydrogenase subunit beta False
MMP0172 CDS 2761846 chromosome 180131 180415 - hypothetical protein MMP0172 False
MMP0347 CDS 2761136 chromosome 343814 344128 - hypothetical protein MMP0347 False
MMP0486 CDS 2761625 chromosome 482858 483295 + hypothetical protein MMP0486 False
MMP0791 CDS 2762263 chromosome 784022 784600 + TetR family transcriptional regulator Member True
MMP0792 CDS 2762239 chromosome 784694 785689 + membrane protein False
MMP0793 CDS 2761683 chromosome 785705 786652 + hypothetical protein MMP0793 False
MMP0799 CDS 2762700 chromosome 791640 792218 + TetR family transcriptional regulator Member True
MMP0818 frcG CDS 2762096 chromosome 812509 813237 - coenzyme F420-reducing hydrogenase subunit gamma False
MMP0819 frcD CDS 2762097 chromosome 813248 813748 - coenzyme F420-reducing hydrogenase subunit delta False
MMP0822 vhcG CDS 2761151 chromosome 815792 816694 + coenzyme F420-non-reducing hydrogenase subunit gamma False
MMP0824 vhcB CDS 2762235 chromosome 818140 819333 + coenzyme F420-non-reducing hydrogenase subunit beta False
MMP1053 hdrB2 CDS 2761166 chromosome 1044633 1045514 - heterodisulfide reductase subunit B2 False
MMP1054 hdrC2 CDS 2762781 chromosome 1045550 1046104 - heterodisulfide reductase subunit C2 False
MMP1297 fdhB CDS 2761363 chromosome 1282622 1283785 - formate dehydrogenase subunit beta False
MMP1298 fdhA CDS 2761025 chromosome 1283821 1285845 - formate dehydrogenase subunit alpha False
MMP1299 CDS 2762229 chromosome 1286147 1286599 - carbonic anhydrase False
MMP1300 CDS 2762230 chromosome 1286620 1287153 - hypothetical protein MMP1300 False
MMP1301 fdhC CDS 2762379 chromosome 1287191 1288015 - formate/nitrite transporter False
MMP1302 CDS 2762343 chromosome 1288260 1288505 - hypothetical protein MMP1302 False
MMP1378 CDS 2761325 chromosome 1358903 1359079 + hypothetical protein MMP1378 False
MMP1642 CDS 2762324 chromosome 1584091 1584645 + ATP/GTP-binding motif-containing protein False
Unanno_18 novel None chromosome 449694 449856 + None False
Unanno_45 novel None chromosome 755625 755743 + None False
Unanno_50 novel None chromosome 835480 835530 + None 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 9

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.