Organism : Methanococcus maripaludis S2 | Module List:
Module 107 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 107

There are 6 regulatory influences for Module 107

Regulator Table (6)
Regulator Name Type
MMP0168
MMP0907		 combiner
MMP0460
MMP1100		 combiner
MMP1100
MMP1442		 combiner
MMP0386
H2		 combiner
MMP1376 tf
MMP1467
MMP1646		 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
871 1.00e-01 tctAtGGtgg
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872 2.40e+02 CCCtccCaGAGCcC
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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 107 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 9/32
Methane metabolism kegg pathway 9.00e-06 1.04e-04 10/32
Metabolic pathways kegg pathway 7.46e-04 3.75e-03 13/32
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 19/32
Metabolism kegg subcategory 5.25e-03 2.02e-02 17/32
Metabolism kegg category 8.90e-05 5.75e-04 21/32
Global kegg category 5.25e-03 2.49e-02 17/32
Metabolism kegg category 1.57e-02 3.92e-02 12/32
Energy Metabolism kegg subcategory 4.90e-05 5.00e-04 10/32
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 9/32
Methane metabolism kegg pathway 9.00e-06 1.08e-04 10/32
Global kegg category 1.23e-03 6.41e-03 13/32
Metabolism kegg subcategory 1.23e-03 6.41e-03 13/32
Metabolic pathways kegg pathway 7.46e-04 4.41e-03 13/32

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
ATP synthesis coupled proton transport biological_process 0.00e+00 0.00e+00 7/32
hydrogen-transporting two-sector ATPase activity molecular_function 0.00e+00 0.00e+00 9/32
electron carrier activity molecular_function 3.65e-03 6.04e-03 4/32
hydrogen ion transporting ATP synthase activity, rotational mechanism molecular_function 0.00e+00 0.00e+00 9/32
proton-transporting ATPase activity, rotational mechanism molecular_function 0.00e+00 0.00e+00 9/32
iron-sulfur cluster binding molecular_function 1.14e-02 1.58e-02 4/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Fe-S-cluster-containing hydrogenase components 2 cog 1.00e-06 1.00e-06 3/32
Energy production and conversion cog subcategory 4.00e-06 1.28e-04 11/32
Transcription cog subcategory 1.94e-02 2.88e-02 3/32
Energy production and conversion cog subcategory 4.00e-06 9.00e-06 11/32
Fe-S-cluster-containing hydrogenase components 2 cog 1.00e-06 1.00e-06 3/32
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 107

There are 32 genes in Module 107

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0014 truD CDS 2762446 chromosome 24061 25230 - tRNA pseudouridine synthase D False
MMP0015 CDS 2762075 chromosome 25243 26046 - hypothetical protein MMP0015 False
MMP0098 CDS 2761685 chromosome 107786 107983 - ferredoxin False
MMP0104 CDS 2762029 chromosome 113747 114364 + polyferredoxin False
MMP0105 CDS 2761334 chromosome 114487 115014 + hypothetical protein MMP0105 False
MMP0106 CDS 2761252 chromosome 115117 115677 + hypothetical protein MMP0106 False
MMP0212 CDS 2761470 chromosome 218916 220640 - glycyl-tRNA synthetase False
MMP0637 CDS 2762062 chromosome 629884 630426 + ArsR family transcriptional regulator True
MMP0873 CDS 2762162 chromosome 864944 866647 + hypothetical protein MMP0873 False
MMP0917 dapF CDS 2761669 chromosome 905897 906730 + diaminopimelate epimerase False
MMP0935 CDS 2762256 chromosome 923434 923931 + hypothetical protein MMP0935 False
MMP0936 aroE CDS 2762259 chromosome 923937 924773 + shikimate 5-dehydrogenase False
MMP1038 atpH CDS 2762089 chromosome 1031411 1031719 + A1A0 ATPase subunit H False
MMP1039 atpI CDS 2762450 chromosome 1031753 1033813 + V-type ATP synthase subunit I False
MMP1040 atpK CDS 2762462 chromosome 1033866 1034534 + V-type ATP synthase subunit K False
MMP1041 atpE CDS 2761185 chromosome 1034595 1035206 + A1A0 ATPase subunit IE False
MMP1042 atpC CDS 2761156 chromosome 1035217 1036392 + V-type ATP synthase subunit C False
MMP1043 atpF CDS 2762703 chromosome 1036414 1036713 + V-type ATP synthase subunit F False
MMP1044 atpA CDS 2762726 chromosome 1036729 1038489 + V-type ATP synthase subunit A False
MMP1045 atpB CDS 2761712 chromosome 1038524 1039912 + V-type ATP synthase subunit B False
MMP1046 atpD CDS 2761313 chromosome 1039959 1040603 + V-type ATP synthase subunit D False
MMP1047 CDS 2761314 chromosome 1040625 1040990 + hypothetical protein MMP1047 False
MMP1190 CDS 2762184 chromosome 1172516 1172968 - FKBP-type peptidylprolyl isomerase False
MMP1219 CDS 2762524 chromosome 1206366 1208375 - putative dinG ATP-dependent helicase False
MMP1337 CDS 2762590 chromosome 1318233 1318715 + hydrogenase maturation protease False
MMP1429 rpm CDS 2761672 chromosome 1401129 1401446 - DNA-directed RNA polymerase subunit M False
MMP1464 ehaQ CDS 2761783 chromosome 1426400 1426885 + hypothetical protein MMP1464 False
MMP1465 ehaR CDS 2761322 chromosome 1426906 1427664 + hypothetical protein MMP1465 False
MMP1466 ehaS CDS 2761323 chromosome 1427680 1428321 + putative CBS domain-containing signal transduction protein False
Unanno_3 novel None chromosome 8261 8419 - None False
Unanno_5 novel None chromosome 16514 16614 - None False
Unanno_60 novel None chromosome 1639283 1639405 + 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.

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.