Organism : Methanococcus maripaludis S2 | Module List:
Module 99 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 99

There are 0 regulatory influences for Module 99

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
855 3.10e+03 CGcaGtTTcCcCTACcGaTAC
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856 4.90e+03 cgTTatctTTttGaTAgGGgCg
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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 99 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nitrogen metabolism kegg pathway 0.00e+00 0.00e+00 8/28
Chloroalkane and chloroalkene degradation kegg pathway 0.00e+00 5.00e-06 3/28
Two-component system kegg pathway 5.00e-06 6.70e-05 4/28
Energy Metabolism kegg subcategory 2.03e-04 1.42e-03 9/28
Xenobiotics Biodegradation and Metabolism kegg subcategory 2.61e-04 1.77e-03 3/28
Signal Transduction kegg subcategory 5.00e-06 5.90e-05 4/28
Metabolism kegg category 3.60e-04 2.13e-03 18/28
Environmental Information Processing kegg category 6.90e-05 4.62e-04 6/28
Energy Metabolism kegg subcategory 7.50e-05 7.29e-04 9/28
Nitrogen metabolism kegg pathway 0.00e+00 0.00e+00 8/28
Xenobiotics Biodegradation and Metabolism kegg subcategory 2.11e-04 1.67e-03 3/28
Chloroalkane and chloroalkene degradation kegg pathway 0.00e+00 6.00e-06 3/28
Environmental Information Processing kegg category 5.70e-05 5.73e-04 6/28
Signal Transduction kegg subcategory 5.00e-06 6.80e-05 4/28
Two-component system kegg pathway 5.00e-06 6.80e-05 4/28

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 7.63e-03 1.09e-02 5/28
regulation of nitrogen utilization biological_process 0.00e+00 0.00e+00 5/28
nitrogen fixation biological_process 0.00e+00 0.00e+00 5/28
nitrogenase activity molecular_function 0.00e+00 0.00e+00 6/28
iron-iron nitrogenase activity molecular_function 0.00e+00 0.00e+00 6/28
molybdenum-iron nitrogenase activity molecular_function 0.00e+00 0.00e+00 6/28
vanadium-iron nitrogenase activity molecular_function 0.00e+00 0.00e+00 6/28
enzyme regulator activity molecular_function 0.00e+00 0.00e+00 5/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Nitrogen fixation tigr sub1role 0.00e+00 1.00e-06 3/28
Central intermediary metabolism tigr mainrole 2.00e-05 8.31e-04 3/28
Transport and binding proteins tigr mainrole 2.36e-03 1.51e-02 3/28
Central intermediary metabolism tigr mainrole 2.00e-05 4.70e-05 3/28
Nitrogen fixation tigr sub1role 0.00e+00 0.00e+00 3/28
Transport and binding proteins tigr mainrole 2.36e-03 3.71e-03 3/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Nitrogen regulatory protein PII cog 0.00e+00 0.00e+00 5/28
Nitrogenase molybdenum-iron protein, alpha and beta chains cog 0.00e+00 0.00e+00 4/28
Amino acid transport and metabolism cog subcategory 2.22e-03 1.95e-02 6/28
Inorganic ion transport and metabolism cog subcategory 8.16e-04 1.06e-02 5/28
Metabolism cog category 5.27e-03 4.57e-02 15/28
Metabolism cog category 3.21e-03 5.10e-03 15/28
Amino acid transport and metabolism cog subcategory 2.22e-03 3.58e-03 6/28
Inorganic ion transport and metabolism cog subcategory 8.16e-04 1.43e-03 5/28
Nitrogen regulatory protein PII cog 0.00e+00 0.00e+00 5/28
Nitrogenase molybdenum-iron protein, alpha and beta chains cog 0.00e+00 0.00e+00 4/28
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 99

There are 28 genes in Module 99

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0064 glnK1 CDS 2761869 chromosome 76751 77089 + nitrogen regulatory protein P-II False
MMP0065 amtB CDS 2761801 chromosome 77116 78342 + ammonium transporter False
MMP0066 glnB CDS 2761915 chromosome 78446 78784 + nitrogen regulatory protein P-II False
MMP0067 glnK2 CDS 2761181 chromosome 78986 79324 + nitrogen regulatory protein P-II False
MMP0068 amtB CDS 2761349 chromosome 79353 80588 + ammonium transporter False
MMP0204 CDS 2761909 chromosome 211471 212001 + hypothetical protein MMP0204 False
MMP0205 modA CDS 2761406 chromosome 212528 213331 + molybdenum ABC transporter periplasmic molybdenum-binding protein False
MMP0456 xerD-like CDS 2761318 chromosome 448553 449101 - Phage integrase False
MMP0480 CDS 2761814 chromosome 475968 476249 + hypothetical protein MMP0480 True
MMP0514 modA CDS 2762212 chromosome 520134 520910 + molybdenum ABC transporter periplasmic molybdate-binding protein False
MMP0853 nifH CDS 2762307 chromosome 844090 844917 + nitrogenase reductase False
MMP0854 NifI1 CDS 2762306 chromosome 844960 845277 + nitrogen regulatory protein P-II False
MMP0855 nifI2 CDS 2761910 chromosome 845287 845652 + nitrogen regulatory protein P-II False
MMP0856 nifD CDS 2761670 chromosome 845702 847135 + nitrogenase subunit alpha False
MMP0857 nifK CDS 2762384 chromosome 847128 848516 + nitrogenase False
MMP0858 nifE CDS 2762315 chromosome 848539 849981 + nitrogenase MoFe cofactor biosynthesis protein NifE False
MMP0859 nifN CDS 2761065 chromosome 849999 851375 + nitrogenase False
MMP0860 nifX CDS 2762059 chromosome 851341 851661 + nitrogen fixation-like protein False
MMP1033 CDS 2761843 chromosome 1025552 1028482 + hypothetical protein MMP1033 False
MMP1049 CDS 2761052 chromosome 1041634 1041903 + multiple resistance and pH regulation protein F False
MMP1091 CDS 2762662 chromosome 1083536 1084384 - ADP-glucose pyrophosphorylase False
MMP1206 glnA CDS 2761968 chromosome 1192748 1194088 + glutamine synthetase False
MMP1388 CDS 2761104 chromosome 1367987 1368232 - redox-active disulfide protein 2 False
MMP1390 CDS 2761449 chromosome 1369544 1369714 - hypothetical protein MMP1390 False
MMP1442 CDS 2761388 chromosome 1413550 1413837 + transcription regulator ArsR True
MMP1576 CDS 2761954 chromosome 1526111 1526266 + hypothetical protein MMP1576 False
Unanno_47 novel None chromosome 776841 776933 - None False
Unanno_6 novel None chromosome 76524 76692 + 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 99

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.