Organism : Methanococcus maripaludis S2 | Module List:
Module 95 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 95

There are 3 regulatory influences for Module 95

Regulator Table (3)
Regulator Name Type
MMP0217
MMP1303
combiner
MMP1100
MMP1646
combiner
MMP1376
MMP1646
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
847 3.20e+01 GGCcaagGCc
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848 5.00e+01 CGaGGgAtaTg
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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 95 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 1.00e-02 2.26e-02 3/33
Carbohydrate Metabolism kegg subcategory 2.18e-03 1.02e-02 7/33
Membrane Transport kegg subcategory 1.46e-02 4.68e-02 3/33
Metabolism kegg category 6.12e-03 2.81e-02 18/33
Environmental Information Processing kegg category 8.51e-03 3.67e-02 4/33
Environmental Information Processing kegg category 7.47e-03 2.26e-02 4/33
Membrane Transport kegg subcategory 1.46e-02 3.76e-02 3/33
ABC transporters kegg pathway 1.00e-02 2.86e-02 3/33

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 2.71e-03 4.82e-03 5/33
ATP binding molecular_function 2.87e-02 3.59e-02 5/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 3.87e-03 3.04e-02 4/33
Inorganic ion transport and metabolism cog subcategory 3.11e-04 4.99e-03 6/33
Transcription cog subcategory 3.87e-03 6.11e-03 4/33
Inorganic ion transport and metabolism cog subcategory 3.11e-04 5.98e-04 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 95

There are 33 genes in Module 95

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0104 CDS 2762029 chromosome 113747 114364 + polyferredoxin False
MMP0108 CDS 2761038 chromosome 116352 117383 + ABC-type Iron(III)-binding periplasmic protein precursor False
MMP0178 purQ CDS 2761716 chromosome 186678 187496 - phosphoribosylformylglycinamidine synthase I False
MMP0216 CDS 2761711 chromosome 222645 224720 - cation transport ATPase False
MMP0253 acd CDS 2762322 chromosome 253586 255694 - CoA-binding domain-containing protein False
MMP0271 CDS 2762176 chromosome 270743 271441 - putative ATP binding nickel incorporation protein False
MMP0354 CDS 2761883 chromosome 349799 351034 + putative oligosaccharide transporter False
MMP0479 CDS 2761495 chromosome 475377 475787 - hypothetical protein MMP0479 False
MMP0849 CDS 2761398 chromosome 840626 841249 + L-lysine/ homoserine-homoserine lactone exporter family protein False
MMP0861 kamA CDS 2762078 chromosome 852237 853538 + lysine 2,3-aminomutase False
MMP0862 yodP CDS 2762074 chromosome 853539 854363 + GCN5-like N-acetyltransferase False
MMP0873 CDS 2762162 chromosome 864944 866647 + hypothetical protein MMP0873 False
MMP0999 CDS 2761900 chromosome 984278 984865 - hypothetical protein MMP0999 False
MMP1000 CDS 2761652 chromosome 984862 985110 - hypothetical protein MMP1000 False
MMP1099 CDS 2762403 chromosome 1091935 1092636 + phosphate transporter PhoU False
MMP1150 mtaA CDS 2762578 chromosome 1139143 1140201 - uroporphyrinogen decarboxylase False
MMP1199 CDS 2761422 chromosome 1185544 1186398 + phosphate transporter PhoU False
MMP1210 CDS 2761760 chromosome 1197303 1197992 + hypothetical protein MMP1210 True
MMP1212 CDS 2761710 chromosome 1199123 1200301 + acetyl-CoA acetyltransferase False
MMP1219 CDS 2762524 chromosome 1206366 1208375 - putative dinG ATP-dependent helicase False
MMP1232 CDS 2761110 chromosome 1219930 1220820 - PP-loop domain-containing protein False
MMP1337 CDS 2762590 chromosome 1318233 1318715 + hydrogenase maturation protease False
MMP1429 rpm CDS 2761672 chromosome 1401129 1401446 - DNA-directed RNA polymerase subunit M False
MMP1466 ehaS CDS 2761323 chromosome 1427680 1428321 + putative CBS domain-containing signal transduction protein False
MMP1612 CDS 2761576 chromosome 1558700 1559377 - hypothetical protein MMP1612 False
MMP1651 modA CDS 2761373 chromosome 1591808 1592611 - molybdenum ABC transporter periplasmic molybdate-binding protein False
MMP1652 CDS 2761934 chromosome 1592694 1593692 - molybdate ABC transporter periplasmic substrate-binding protein False
Unanno_12 novel None chromosome 253208 253542 - None False
Unanno_24 novel None chromosome 473191 473357 + None False
Unanno_28 novel None chromosome 478373 478437 + None False
Unanno_49 novel None chromosome 835256 835308 + None False
Unanno_5 novel None chromosome 16514 16614 - None False
Unanno_60 novel None chromosome 1639283 1639405 + 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 95

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.