Organism : Methanococcus maripaludis S2 | Module List:
Module 104 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 104

There are 2 regulatory influences for Module 104

Regulator Table (2)
Regulator Name Type
MMP0097
MMP1467		 combiner
MMP0032
MMP0907		 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
865 3.00e+02 tgtAAc.gttccTGg
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866 3.10e+03 cCCCCG
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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 104 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Purine metabolism kegg pathway 6.54e-03 1.64e-02 3/30
Nucleotide Metabolism kegg subcategory 2.93e-03 1.26e-02 5/30
Metabolism of Cofactors and Vitamins kegg subcategory 2.72e-03 1.18e-02 4/30
Nucleotide Metabolism kegg subcategory 4.58e-03 1.59e-02 4/30
Purine metabolism kegg pathway 6.54e-03 2.05e-02 3/30
Metabolism of Cofactors and Vitamins kegg subcategory 2.72e-03 1.12e-02 4/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 4.13e-02 4.93e-02 3/30
catalytic activity molecular_function 3.69e-03 6.04e-03 4/30
DNA-directed DNA polymerase activity molecular_function 0.00e+00 0.00e+00 14/30
iron-sulfur cluster binding molecular_function 8.61e-03 1.25e-02 4/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Methanogenesis tigr sub1role 9.82e-04 2.89e-03 3/30
Energy metabolism tigr mainrole 1.65e-02 4.36e-02 3/30
Unknown function tigr mainrole 3.07e-03 1.75e-02 3/30
Energy metabolism tigr mainrole 1.65e-02 2.10e-02 3/30
Methanogenesis tigr sub1role 9.82e-04 1.70e-03 3/30
Unknown function tigr mainrole 3.07e-03 4.71e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Coenzyme transport and metabolism cog subcategory 1.41e-03 1.45e-02 6/30
Coenzyme transport and metabolism cog subcategory 1.41e-03 2.36e-03 6/30
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 104

There are 30 genes in Module 104

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Antisense_1 novel None chromosome 107797 108023 + None False
MMP0011 CDS 2761978 chromosome 20974 22041 - DNA-cytosine methyltransferase False
MMP0019 CDS 2761254 chromosome 28670 28897 - hypothetical protein MMP0019 False
MMP0077 CDS 2762119 chromosome 87961 88689 + radical SAM domain-containing protein False
MMP0125 flpA CDS 2761698 chromosome 130979 132511 - fibrillarin-like protein False
MMP0126 bioB CDS 2761717 chromosome 132540 133565 - biotin synthase False
MMP0161 comB CDS 2761804 chromosome 170597 171343 - 2-phosphosulfolactate phosphatase False
MMP0170 cofF CDS 2761868 chromosome 178521 179378 + RimK family alpha-L-glutamate ligase False
MMP0186 CDS 2761228 chromosome 194539 195159 + hypothetical protein MMP0186 False
MMP0214 CDS 2761131 chromosome 221545 222096 - putative deoxyribonucleotide triphosphate pyrophosphatase False
MMP0218 CDS 2762538 chromosome 225098 225925 + hypothetical protein MMP0218 False
MMP0236 CDS 2762595 chromosome 243562 243960 + hypothetical protein MMP0236 False
MMP0379 CDS 2761650 chromosome 376162 376485 - hypothetical protein MMP0379 False
MMP0380 dnaB CDS 2762557 chromosome 376490 378844 - DNA polymerase family B protein False
MMP0392 purD CDS 2762213 chromosome 389726 391060 - phosphoribosylamine--glycine ligase False
MMP0731 CDS 2761234 chromosome 724442 724645 - exodeoxyribonuclease VII small subunit False
MMP0895 CDS 2761429 chromosome 888224 888832 + hypothetical protein MMP0895 False
MMP0909 CDS 2761840 chromosome 901906 902388 + hypothetical protein MMP0909 False
MMP0986 thyA CDS 2762338 chromosome 972543 973418 - thymidylate synthase False
MMP1027 CDS 2761182 chromosome 1018191 1018742 - hypothetical protein MMP1027 False
MMP1202 CDS 2762356 chromosome 1188662 1189069 - hypothetical protein MMP1202 False
MMP1203 cbiD CDS 2762357 chromosome 1189053 1190150 - cobalt-precorrin-6A synthase False
MMP1232 CDS 2761110 chromosome 1219930 1220820 - PP-loop domain-containing protein False
MMP1264 CDS 2761465 chromosome 1246831 1248324 - hypothetical protein MMP1264 False
MMP1350 CDS 2762419 chromosome 1329745 1331058 - radical SAM domain-containing protein False
MMP1377 CDS 2761324 chromosome 1357616 1358683 + hypothetical protein MMP1377 False
MMP1485 moaB CDS 2761750 chromosome 1444866 1445351 + molybdenum cofactor biosynthesis protein False
MMP1494 CDS 2761058 chromosome 1455296 1455910 + hypothetical protein MMP1494 False
MMP1600 CDS 2762351 chromosome 1547994 1548800 - ribosomal protein S6 modification protein False
Unanno_59 novel None chromosome 1574438 1574532 + 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.