Organism : Methanococcus maripaludis S2 | Module List:
Module 123 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 123

There are 4 regulatory influences for Module 123

Regulator Table (4)
Regulator Name Type
MMP0052
MMP0480		 combiner
H2 ef
MMP0097
MMP0527		 combiner
MMP0086
MMP0097		 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
899 1.50e+03 TGaGacACatCgGc.G
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900 4.60e+03 TtGAatTTaAAAc
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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 123 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Microbial metabolism in diverse environments kegg pathway 1.32e-02 2.71e-02 6/33
Energy Metabolism kegg subcategory 1.32e-02 4.28e-02 7/33
Microbial metabolism in diverse environments kegg pathway 1.32e-02 3.48e-02 6/33

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 4.22e-03 6.83e-03 6/33
metabolic process biological_process 1.37e-02 1.77e-02 4/33
catalytic activity molecular_function 5.66e-03 8.70e-03 4/33
electron carrier activity molecular_function 4.19e-03 6.78e-03 4/33
FMN binding molecular_function 9.00e-06 3.20e-05 3/33
oxidoreductase activity molecular_function 2.16e-03 3.88e-03 3/33
iron-sulfur cluster binding molecular_function 1.29e-02 1.77e-02 4/33
CoB--CoM heterodisulfide reductase activity molecular_function 2.00e-06 7.00e-06 3/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 2.29e-02 2.82e-02 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Predicted transcriptional regulator with C-terminal CBS domains cog 1.00e-06 1.00e-06 3/33
Transcription cog subcategory 3.87e-03 3.04e-02 4/33
Energy production and conversion cog subcategory 1.05e-03 1.22e-02 8/33
Transcription cog subcategory 3.87e-03 6.11e-03 4/33
Energy production and conversion cog subcategory 1.05e-03 1.79e-03 8/33
Predicted transcriptional regulator with C-terminal CBS domains cog 1.00e-06 1.00e-06 3/33
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 123

There are 33 genes in Module 123

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0020 CDS 2761587 chromosome 28989 29414 - nickel responsive regulator True
MMP0123 purT CDS 2762130 chromosome 129070 130236 + phosphoribosylglycinamide formyltransferase 2 False
MMP0624 CDS 2761591 chromosome 618397 618798 + hypothetical protein MMP0624 False
MMP0628 CDS 2761600 chromosome 620371 620577 + TOBE domain-containing protein False
MMP0683 ftsY CDS 2762618 chromosome 671197 672348 - signal recognition particle-docking protein FtsY False
MMP0763 CDS 2761230 chromosome 753774 754082 + hypothetical protein MMP0763 False
MMP0772 CDS 2762765 chromosome 762949 763713 - hypothetical protein MMP0772 False
MMP0820 frcA CDS 2762313 chromosome 813762 814994 - coenzyme F420-reducing hydrogenase subunit alpha False
MMP0825 hdrA CDS 2762216 chromosome 819424 821388 + heterodisulfide reductase subunit A False
MMP0908 CDS 2761908 chromosome 901511 901891 + CBS domain-containing protein False
MMP1016 CDS 2761957 chromosome 1003113 1004354 + putative CBS domain-containing signal transduction protein False
MMP1067 CDS 2762543 chromosome 1058824 1060308 - succinate dehydrogenase/fumarate reductase iron-sulfur subunit False
MMP1134 CDS 2762091 chromosome 1123998 1125221 + type A flavoprotein False
MMP1135 CDS 2762102 chromosome 1125405 1126625 + flavodoxin:beta-lactamase-like False
MMP1136 CDS 2762103 chromosome 1126811 1127230 + rubrerythrin False
MMP1154 hdrC1 CDS 2761626 chromosome 1142799 1143377 + heterosulfide reductase subunit C1 False
MMP1156 CDS 2761281 chromosome 1144326 1144640 + carboxymuconolactone decarboxylase False
MMP1158 CDS 2761825 chromosome 1145031 1145297 + hypothetical protein MMP1158 False
MMP1223 CDS 2762267 chromosome 1211914 1213392 - hypothetical protein MMP1223 False
MMP1229 CDS 2761117 chromosome 1217998 1218300 + FUN14 family protein False
MMP1251 CDS 2762571 chromosome 1234459 1235019 + putative CBS domain-containing signal transduction protein False
MMP1252 CDS 2762572 chromosome 1235042 1235881 + CBS domain-containing protein False
MMP1347 HMmB CDS 2762407 chromosome 1327452 1327652 - histone B True
MMP1439 CDS 2761971 chromosome 1410479 1411699 + cofactor-independent phosphoglycerate mutase False
MMP1533 CDS 2762783 chromosome 1491966 1492418 + hypothetical protein MMP1533 False
MMP1534 CDS 2762784 chromosome 1492583 1492972 + hypothetical protein MMP1534 False
MMP1642 CDS 2762324 chromosome 1584091 1584645 + ATP/GTP-binding motif-containing protein False
MMP1660 CDS 2761437 chromosome 1604456 1604815 + hypothetical protein MMP1660 False
MMP1661 CDS 2761119 chromosome 1604805 1605002 + hypothetical protein MMP1661 False
MMP1685 CDS 2761610 chromosome 1627151 1627375 - hypothetical protein MMP1685 False
MMP1697 hdrA CDS 2762636 chromosome 1636988 1638964 - heterodisulfide reductase subunit A False
Unanno_32 novel None chromosome 543422 543677 + None False
Unanno_38 novel None chromosome 705953 706017 + 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.