Organism : Methanococcus maripaludis S2 | Module List:
Module 98 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 98

There are 5 regulatory influences for Module 98

Regulator Table (5)
Regulator Name Type
MMP0257
MMP1499
combiner
MMP0257
MMP1210
combiner
MMP0791 tf
MMP0480
MMP1467
combiner
MMP0257
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
853 2.40e-05 ACctAcAtAAAaAc
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854 3.30e+03 ccCGcctATCaGGaG
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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 98 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Two-component system kegg pathway 0.00e+00 0.00e+00 8/24
Bacterial chemotaxis kegg pathway 0.00e+00 0.00e+00 11/24
Signal Transduction kegg subcategory 0.00e+00 0.00e+00 8/24
Cell Motility kegg subcategory 0.00e+00 0.00e+00 11/24
Environmental Information Processing kegg category 0.00e+00 1.00e-06 8/24
Cellular Processes kegg category 0.00e+00 0.00e+00 11/24
Environmental Information Processing kegg category 0.00e+00 2.00e-06 8/24
Signal Transduction kegg subcategory 0.00e+00 0.00e+00 8/24
Two-component system kegg pathway 0.00e+00 0.00e+00 8/24
Cellular Processes kegg category 0.00e+00 0.00e+00 11/24
Cell Motility kegg subcategory 0.00e+00 0.00e+00 11/24
Bacterial chemotaxis kegg pathway 0.00e+00 0.00e+00 11/24

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
two-component signal transduction system (phosphorelay) biological_process 0.00e+00 0.00e+00 3/24
chemotaxis biological_process 0.00e+00 0.00e+00 6/24
signal transduction biological_process 0.00e+00 0.00e+00 4/24
signal transducer activity molecular_function 0.00e+00 0.00e+00 4/24

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Methyl-accepting chemotaxis protein cog 0.00e+00 0.00e+00 3/24
Signal transduction mechanisms cog subcategory 0.00e+00 0.00e+00 11/24
Cell motility cog subcategory 0.00e+00 0.00e+00 14/24
Intracellular trafficking, secretion, and vesicular transport cog subcategory 1.71e-04 3.10e-03 3/24
Cellular processes and signaling cog category 0.00e+00 0.00e+00 28/24
Cellular processes and signaling cog category 0.00e+00 0.00e+00 15/24
Signal transduction mechanisms cog subcategory 0.00e+00 0.00e+00 11/24
Cell motility cog subcategory 0.00e+00 0.00e+00 14/24
Intracellular trafficking, secretion, and vesicular transport cog subcategory 1.71e-04 3.56e-04 3/24
Methyl-accepting chemotaxis protein cog 0.00e+00 0.00e+00 3/24
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 98

There are 24 genes in Module 98

Gene Member Table (24)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
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
MMP0342 CDS 2761456 chromosome 339432 339866 + hypothetical protein MMP0342 False
MMP0413 CDS 2761639 chromosome 411833 414028 + hypothetical protein MMP0413 False
MMP0487 CDS 2761059 chromosome 483526 485715 + hypothetical protein MMP0487 False
MMP0922 CDS 2761317 chromosome 911058 911723 + putative phage infection protein False
MMP0923 dapB CDS 2761082 chromosome 911732 912544 + dihydrodipicolinate reductase False
MMP0924 CDS 2761173 chromosome 912553 913155 + hypothetical protein MMP0924 False
MMP0925 cheW CDS 2761308 chromosome 913166 913609 + chemotaxis protein CheW False
MMP0926 cheB CDS 2761703 chromosome 913654 914751 + response regulator receiver modulated CheB methylesterase False
MMP0927 cheA CDS 2761290 chromosome 914756 917518 + CheA signal transduction histidine kinase False
MMP0928 cheD CDS 2761315 chromosome 917529 917993 + chemoreceptor glutamine deamidase CheD False
MMP0929 CDS 2761083 chromosome 917974 919413 + methyl-accepting chemotaxis sensory transducer False
MMP0930 cheR CDS 2762264 chromosome 919439 920251 - chemotaxis protein CheR False
MMP0931 CDS 2761239 chromosome 920322 920930 - MCP methylation inhibitor CheC False
MMP0932 CDS 2761785 chromosome 920951 921640 - MCP methylation inhibitor CheC False
MMP0933 cheY CDS 2761705 chromosome 921656 922027 - response regulator receiver protein False
MMP0945 CDS 2762612 chromosome 931400 933241 + glyceraldehyde-3-phosphate ferredoxin oxidoreductase False
MMP1230 CDS 2762278 chromosome 1218373 1219431 + DNA polymerase, beta-like region False
MMP1231 CDS 2761109 chromosome 1219505 1219909 + HAD family hydrolase fragment False
MMP1674 flaH CDS 2761721 chromosome 1614821 1615513 + flagellar accessory protein FlaH False
MMP1675 flaI CDS 2761174 chromosome 1615523 1617163 + type II secretion system protein E False
MMP1676 flaJ CDS 2761175 chromosome 1617174 1618850 + flagellar assembly protein J False
MMP1719 CDS 2761040 chromosome 1654837 1657491 - hypothetical protein MMP1719 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 98

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.