Organism : Methanococcus maripaludis S2 | Module List:
Module 35 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 35

There are 4 regulatory influences for Module 35

Regulator Table (4)
Regulator Name Type
MMP1275
MMP1376		 combiner
MMP0637
MMP1015		 combiner
MMP0041
MMP1275		 combiner
MMP0637
MMP1376		 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
731 6.90e-04 ACcgcTaAATCGtTTTTaAAAT
Loader icon
732 1.60e+00 ACTAacttaaTAAATatg.CTTT
Loader icon
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 35 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 4.00e-06 5.70e-05 10/30
Metabolic pathways kegg pathway 4.45e-03 1.26e-02 11/30
Microbial metabolism in diverse environments kegg pathway 8.00e-06 1.02e-04 10/30
Energy Metabolism kegg subcategory 1.20e-05 1.16e-04 11/30
Metabolism kegg subcategory 1.00e-06 1.30e-05 22/30
Metabolism kegg category 1.16e-02 4.73e-02 16/30
Global kegg category 1.00e-06 9.00e-06 22/30
Metabolism kegg category 2.75e-03 1.13e-02 13/30
Energy Metabolism kegg subcategory 3.00e-06 4.90e-05 11/30
Methane metabolism kegg pathway 4.00e-06 5.80e-05 10/30
Global kegg category 2.05e-03 9.15e-03 12/30
Metabolism kegg subcategory 2.05e-03 9.15e-03 12/30
Metabolic pathways kegg pathway 4.45e-03 1.56e-02 11/30
Microbial metabolism in diverse environments kegg pathway 8.00e-06 1.06e-04 10/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
sodium ion transport biological_process 0.00e+00 1.00e-06 4/30
methanogenesis biological_process 2.00e-06 1.30e-05 4/30
tetrahydromethanopterin S-methyltransferase activity molecular_function 0.00e+00 0.00e+00 8/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Methanogenesis tigr sub1role 9.82e-04 2.89e-03 3/30
Energy metabolism tigr mainrole 3.55e-04 5.06e-03 5/30
Energy metabolism tigr mainrole 3.55e-04 6.80e-04 5/30
Methanogenesis tigr sub1role 9.82e-04 1.70e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 1.11e-03 1.26e-02 4/30
Coenzyme transport and metabolism cog subcategory 0.00e+00 1.90e-05 10/30
Cellular processes and signaling cog category 1.51e-02 2.27e-02 6/30
Posttranslational modification, protein turnover, chaperones cog subcategory 1.11e-03 1.89e-03 4/30
Coenzyme transport and metabolism cog subcategory 0.00e+00 1.00e-06 10/30
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 35

There are 30 genes in Module 35

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0076 CDS 2761963 chromosome 87608 87817 - deoxyribonuclease False
MMP0077 CDS 2762119 chromosome 87961 88689 + radical SAM domain-containing protein False
MMP0219 ppaC CDS 2761374 chromosome 226294 227217 + putative manganese-dependent inorganic pyrophosphatase False
MMP0383 slp CDS 2761159 chromosome 381781 383508 + S-layer protein False
MMP0590 CDS 2761039 chromosome 587336 588034 - glycosyl transferase family protein False
MMP0591 CDS 2761417 chromosome 588068 588727 - hypothetical protein MMP0591 False
MMP0592 CDS 2762757 chromosome 588738 588920 - hypothetical protein MMP0592 False
MMP0593 CDS 2762521 chromosome 588917 589702 - walker type ATPase False
MMP0718 CDS 2762016 chromosome 711235 711585 + hypothetical protein MMP0718 False
MMP0719 CDS 2761984 chromosome 711623 712030 + transcriptional regluator True
MMP1073 ehbC CDS 2761687 chromosome 1064872 1065126 + putative monovalent cation/H+ antiporter subunit G False
MMP1190 CDS 2762184 chromosome 1172516 1172968 - FKBP-type peptidylprolyl isomerase False
MMP1191 mch CDS 2762185 chromosome 1173159 1174130 + N(5),N(10)-methenyltetrahydromethanopterin cyclohydrolase False
MMP1373 purP CDS 2762237 chromosome 1354441 1355526 - 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase False
MMP1493 CDS 2761057 chromosome 1453865 1455208 + hypothetical protein MMP1493 False
MMP1518 CDS 2761047 chromosome 1477790 1478728 - sulfate/molybdate ABC-transporter ATPase subunit False
MMP1519 CDS 2761298 chromosome 1478743 1479510 - anion transport system permease False
MMP1520 CDS 2761662 chromosome 1479677 1480351 + hydrogenase accessory protein HypB False
MMP1560 mtrE CDS 2761114 chromosome 1514893 1515792 + tetrahydromethanopterin S-methyltransferase subunit E False
MMP1561 mtrD CDS 2761421 chromosome 1515819 1516526 + tetrahydromethanopterin S-methyltransferase subunit D False
MMP1562 mtrC CDS 2762467 chromosome 1516564 1517352 + tetrahydromethanopterin S-methyltransferase subunit C False
MMP1563 mtrB CDS 2762348 chromosome 1517363 1517689 + tetrahydromethanopterin S-methyltransferase subunit B False
MMP1564 mtrA CDS 2761895 chromosome 1517711 1518430 + tetrahydromethanopterin S-methyltransferase subunit A False
MMP1565 or900 CDS 2762291 chromosome 1518447 1519208 + tetrahydromethanopterin S-methyltransferase subunit A False
MMP1566 mtrG CDS 2761385 chromosome 1519213 1519437 + tetrahydromethanopterin S-methyltransferase subunit G False
MMP1567 mtrH CDS 2761871 chromosome 1519462 1520421 + tetrahydromethanopterin S-methyltransferase subunit H False
MMP1643 CDS 2762325 chromosome 1584652 1585041 + hypothetical protein MMP1643 False
MMP1644 CDS 2762298 chromosome 1585066 1585917 + hypothetical protein MMP1644 False
MMP1717 CDS 2762584 chromosome 1653262 1654344 - type 12 methyltransferase False
MMP1718 CDS 2762585 chromosome 1654349 1654681 - hypothetical protein MMP1718 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.