Organism : Methanococcus maripaludis S2 | Module List:
Module 58 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 58

There are 4 regulatory influences for Module 58

Regulator Table (4)
Regulator Name Type
MMP0907 tf
MMP1015 tf
MMP0168 tf
MMP0629
MMP1015
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
777 3.90e-01 accTaCAaaaatAca.tatAt
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778 1.20e+03 CGTTTCCTCGTGCAC
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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 58 is enriched for following functions.

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
oxidoreductase activity molecular_function 2.16e-03 3.88e-03 3/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 3.52e-03 1.87e-02 3/33
Energy metabolism tigr mainrole 2.29e-02 2.82e-02 3/33
Amino acid biosynthesis tigr mainrole 3.52e-03 5.33e-03 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 1.34e-04 2.58e-03 4/33
Cell motility cog subcategory 1.64e-03 1.61e-02 3/33
Amino acid transport and metabolism cog subcategory 6.00e-03 4.15e-02 6/33
Transcription cog subcategory 2.16e-02 3.19e-02 3/33
Signal transduction mechanisms cog subcategory 1.34e-04 2.87e-04 4/33
Cell motility cog subcategory 1.64e-03 2.71e-03 3/33
Amino acid transport and metabolism cog subcategory 6.00e-03 9.34e-03 6/33
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 58

There are 33 genes in Module 58

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Antisense_3 novel None chromosome 344972 345212 + None False
MMP0050 ribH CDS 2761568 chromosome 66371 66784 + 6,7-dimethyl-8-ribityllumazine synthase False
MMP0051 hisE CDS 2762532 chromosome 66822 67112 + phosphoribosyl-ATP pyrophosphatase False
MMP0059 CDS 2762070 chromosome 73629 74051 - hypothetical protein MMP0059 False
MMP0096 CDS 2762386 chromosome 105895 107082 - putative GntR family transcriptional regulator False
MMP0097 CDS 2762377 chromosome 107207 107755 + transcriptional regulator True
MMP0180 ribC CDS 2761161 chromosome 190641 191111 - riboflavin synthase False
MMP0181 CDS 2762638 chromosome 191240 191779 - hypothetical protein MMP0181 False
MMP0209 CDS 2761303 chromosome 216559 217113 - hypothetical protein MMP0209 True
MMP0210 CDS 2762413 chromosome 217251 218150 + hypothetical protein MMP0210 False
MMP0256 hisH CDS 2762179 chromosome 258316 258927 - imidazole glycerol phosphate synthase subunit HisH False
MMP0257 tbp CDS 2762177 chromosome 258939 259484 - transcription factor True
MMP0369 CDS 2761536 chromosome 364974 366938 + hypothetical protein MMP0369 False
MMP0480 CDS 2761814 chromosome 475968 476249 + hypothetical protein MMP0480 True
MMP0487 CDS 2761059 chromosome 483526 485715 + hypothetical protein MMP0487 False
MMP0524 CDS 2761593 chromosome 530045 530629 - hypothetical protein MMP0524 False
MMP0613 CDS 2761418 chromosome 608278 609078 + acetolactate decarboxylase False
MMP0712 CDS 2762743 chromosome 705074 705820 + amino acid ABC transporter substrate-binding protein False
MMP0722 CDS 2762034 chromosome 714749 715381 + hypothetical protein MMP0722 False
MMP0734 CDS 2761089 chromosome 727487 727804 + hypothetical protein MMP0734 False
MMP0757 CDS 2761345 chromosome 749567 749875 - hypothetical protein MMP0757 False
MMP0788 CDS 2762337 chromosome 778818 780980 + hypothetical protein MMP0788 False
MMP0922 CDS 2761317 chromosome 911058 911723 + putative phage infection protein False
MMP0923 dapB CDS 2761082 chromosome 911732 912544 + dihydrodipicolinate reductase False
MMP0932 CDS 2761785 chromosome 920951 921640 - MCP methylation inhibitor CheC 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
MMP1229 CDS 2761117 chromosome 1217998 1218300 + FUN14 family protein False
MMP1439 CDS 2761971 chromosome 1410479 1411699 + cofactor-independent phosphoglycerate mutase False
MMP1493 CDS 2761057 chromosome 1453865 1455208 + hypothetical protein MMP1493 False
MMP1550 CDS 2762528 chromosome 1503803 1504474 + NADP oxidoreductase, coenzyme F420-dependent False
Unanno_47 novel None chromosome 776841 776933 - 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 58

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.