Organism : Methanococcus maripaludis S2 | Module List:
Module 66 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 66

There are 1 regulatory influences for Module 66

Regulator Table (1)
Regulator Name Type
MMP1467 tf

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
793 4.50e+02 TttCTtt..tA.aATccccG
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794 1.70e+03 GaTGCAGT
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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 66 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Methane metabolism kegg pathway 5.90e-05 5.53e-04 9/32
ABC transporters kegg pathway 1.32e-04 1.08e-03 5/32
Energy Metabolism kegg subcategory 6.98e-04 4.29e-03 9/32
Membrane Transport kegg subcategory 2.44e-04 1.67e-03 5/32
Metabolism kegg category 1.24e-03 6.57e-03 19/32
Environmental Information Processing kegg category 1.74e-04 1.11e-03 6/32
Metabolism kegg category 3.00e-05 3.32e-04 17/32
Energy Metabolism kegg subcategory 2.70e-04 1.99e-03 9/32
Methane metabolism kegg pathway 5.90e-05 5.91e-04 9/32
Environmental Information Processing kegg category 1.06e-03 5.72e-03 5/32
Membrane Transport kegg subcategory 2.44e-04 1.83e-03 5/32
ABC transporters kegg pathway 1.32e-04 1.16e-03 5/32

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
phosphate ion transport biological_process 1.00e-06 3.00e-06 3/32
inorganic phosphate transmembrane transporter activity molecular_function 0.00e+00 0.00e+00 3/32

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Anions tigr sub1role 0.00e+00 1.00e-06 5/32
Transport and binding proteins tigr mainrole 2.00e-06 1.78e-04 6/32
Transport and binding proteins tigr mainrole 2.00e-06 6.00e-06 6/32
Anions tigr sub1role 0.00e+00 0.00e+00 5/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Inorganic ion transport and metabolism cog subcategory 1.72e-03 1.65e-02 5/32
Function unknown cog subcategory 3.35e-03 2.70e-02 8/32
Metabolism cog category 6.60e-03 1.03e-02 16/32
Inorganic ion transport and metabolism cog subcategory 1.72e-03 2.82e-03 5/32
Function unknown cog subcategory 3.35e-03 5.32e-03 8/32
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 66

There are 32 genes in Module 66

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0014 truD CDS 2762446 chromosome 24061 25230 - tRNA pseudouridine synthase D False
MMP0015 CDS 2762075 chromosome 25243 26046 - hypothetical protein MMP0015 False
MMP0022 CDS 2761246 chromosome 30411 30746 - hypothetical protein MMP0022 False
MMP0023 CDS 2761056 chromosome 30743 31567 - hypothetical protein MMP0023 False
MMP0179 purL CDS 2761152 chromosome 187497 190466 - phosphoribosylformylglycinamidine synthase False
MMP0609 pth2 CDS 2762305 chromosome 604474 604824 - peptidyl-tRNA hydrolase False
MMP0844 CDS 2761720 chromosome 837505 838239 + hypothetical protein MMP0844 False
MMP0868 proV CDS 2761562 chromosome 859546 860715 - ABC transporter ATPase False
MMP0936 aroE CDS 2762259 chromosome 923937 924773 + shikimate 5-dehydrogenase False
MMP0945 CDS 2762612 chromosome 931400 933241 + glyceraldehyde-3-phosphate ferredoxin oxidoreductase False
MMP1034 tmk CDS 2761844 chromosome 1028504 1029103 + thymidylate kinase False
MMP1082 hisH CDS 2761201 chromosome 1073455 1074063 + imidazole glycerol phosphate synthase subunit HisH False
MMP1090 CDS 2761155 chromosome 1082533 1083453 - NAD-dependent epimerase/dehydratase False
MMP1095 CDS 2761791 chromosome 1088405 1089244 + phosphate-binding protein False
MMP1096 CDS 2761405 chromosome 1089326 1090201 + phosphate ABC transporter inner membrane protein False
MMP1097 CDS 2762309 chromosome 1090214 1091080 + phosphate ABC transporter inner membrane protein False
MMP1098 pstB CDS 2761654 chromosome 1091100 1091855 + phosphate ABC transporter ATP-binding protein False
MMP1099 CDS 2762403 chromosome 1091935 1092636 + phosphate transporter PhoU False
MMP1171 pssA CDS 2762502 chromosome 1154613 1155227 + CDP-diacylglycerol--serine O-phosphatidyltransferase False
MMP1303 CDS 2762382 chromosome 1288715 1290634 - sensory transduction histidine kinase True
MMP1454 ehaG CDS 2762111 chromosome 1420103 1420789 + hypothetical protein MMP1454 False
MMP1455 ehaH CDS 2762107 chromosome 1420811 1421473 + putative transmembrane subunit of a hydrogenase False
MMP1456 ehaI CDS 2762124 chromosome 1421483 1421692 + hypothetical protein MMP1456 False
MMP1457 ehaJ CDS 2761365 chromosome 1421694 1422572 + energy conserving hydrogenase A integral membrane subunit False
MMP1458 ehaK CDS 2761443 chromosome 1422581 1422832 + hypothetical protein MMP1458 False
MMP1459 ehaL CDS 2762288 chromosome 1422837 1423136 + hypothetical protein MMP1459 False
MMP1460 ehaM CDS 2762168 chromosome 1423152 1423562 + hypothetical protein MMP1460 False
MMP1462 ehaO CDS 2761336 chromosome 1424070 1425197 + energy conserving hydrogenase A large subunit False
MMP1463 ehaP CDS 2761337 chromosome 1425226 1426407 + polyferredoxin False
MMP1531 CDS 2762604 chromosome 1489235 1490206 - hypothetical protein MMP1531 False
MMP1662 cbiF CDS 2761120 chromosome 1604999 1605763 - precorrin-4 C11-methyltransferase False
MMP1665 CDS 2762589 chromosome 1607978 1609843 - HEAT domain-containing protein 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.