Organism : Methanococcus maripaludis S2 | Module List:
Module 101 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 101

There are 0 regulatory influences for Module 101

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
859 0.00e+00 CaGgCTggaC.Acc
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860 1.30e+02 aaCacttTTcaAAGGcc.ac
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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 101 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Aminoacyl-tRNA biosynthesis kegg pathway 0.00e+00 0.00e+00 19/37
Translation kegg subcategory 0.00e+00 0.00e+00 22/37
Genetic Information Processing kegg category 0.00e+00 0.00e+00 23/37
Genetic Information Processing kegg category 0.00e+00 0.00e+00 23/37
Translation kegg subcategory 0.00e+00 0.00e+00 22/37
Aminoacyl-tRNA biosynthesis kegg pathway 0.00e+00 0.00e+00 19/37

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 101

There are 37 genes in Module 101

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0139 fdhB CDS 2762396 chromosome 147092 148219 + formate dehydrogenase subunit beta False
MMP0254 CDS 2761399 chromosome 255837 257360 + carbohydrate kinase False
MMP0459 CDS 2761706 chromosome 454461 454838 + hypothetical protein MMP0459 False
MMP0509 fmdA CDS 2761697 chromosome 512896 514647 + formylmethanofuran dehydrogenase subunit A False
MMP0512 fmdB CDS 2762514 chromosome 517360 518697 + molybdenum containing formylmethanofuran dehydrogenase subunit B False
MMP1684 CDS 2762106 chromosome 1626448 1627131 - metallophosphoesterase False
RNA_1 tRNA-Gln1 trna 2761904 chromosome 82518 82593 + Gln tRNA False
RNA_13 tRNA-Ser1 trna 2762525 chromosome 454031 454115 + Ser tRNA False
RNA_14 tRNA-Arg2 trna 2761427 chromosome 700097 700170 + Arg tRNA False
RNA_16 tRNA-Ser2 trna 2762734 chromosome 1305759 1305846 + Ser tRNA False
RNA_19 tRNA-Met1 trna 2761561 chromosome 1507940 1508054 + Met tRNA False
RNA_2 tRNA-Thr1 trna 2761713 chromosome 112878 112951 + Thr tRNA False
RNA_20 tRNA-Phe1 trna 2762197 chromosome 1601495 1601568 + Phe tRNA False
RNA_22 tRNA-Met2 trna 2761193 chromosome 1601189 1601263 - Met tRNA False
RNA_23 tRNA-Glu2 trna 2762568 chromosome 1601100 1601174 - Glu tRNA False
RNA_24 tRNA-Leu2 trna 2762116 chromosome 1601002 1601086 - Leu tRNA False
RNA_26 tRNA-Leu3 trna 2762762 chromosome 1507726 1507810 - Leu tRNA False
RNA_27 tRNA-Val2 trna 2761802 chromosome 1431053 1431129 - Val tRNA False
RNA_3 tRNA-Pro1 trna 2762742 chromosome 112998 113074 + Pro tRNA False
RNA_31 tRNA-Ala1 trna 2762439 chromosome 1049891 1049964 - Ala tRNA False
RNA_43 tRNA-Trp trna 2762716 chromosome 1627513 1627676 - Trp tRNA False
RNA_45 RNaseP rna 2762141 chromosome 36828 37057 - None False
RNA_46 rrnA5S rrna 2761996 chromosome 68 182 - 5S ribosomal RNA False
RNA_47 rrnB5S rrna 2761112 chromosome 5109 5223 - 5S ribosomal RNA False
RNA_48 rnnC5S rrna 2762753 chromosome 37119 37233 - 5S ribosomal RNA False
RNA_49 srp rna 2762535 chromosome 1461663 1461969 + None False
RNA_5 tRNA-Lys1 trna 2761534 chromosome 113173 113246 + Lys tRNA False
RNA_6 tRNA-Asp1 trna 2761359 chromosome 113418 113492 + Asp tRNA False
RNA_7 tRNA-Lys2 trna 2761348 chromosome 113526 113599 + Lys tRNA False
RNA_8 tRNA-Asp2 trna 2762134 chromosome 113620 113694 + Asp tRNA False
Unanno_11 novel None chromosome 226001 226195 - None False
Unanno_23 novel None chromosome 455604 455740 - None False
Unanno_27 novel None chromosome 475135 475331 - None False
Unanno_34 novel None chromosome 573322 573452 + None False
Unanno_35 novel None chromosome 609838 609904 - None False
Unanno_48 novel None chromosome 821487 821569 - None False
Unanno_54 novel None chromosome 941621 941719 - 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 101

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.