Organism : Methanococcus maripaludis S2 | Module List:
Module 8 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 8

There are 5 regulatory influences for Module 8

Regulator Table (5)
Regulator Name Type
MMP1210
MMP1646
combiner
MMP0217
MMP1646
combiner
H2 ef
MMP0465
Formate
combiner
MMP1304 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
677 6.30e-02 cccgcaGgTTCaactcccccTccc
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678 8.30e-01 aGGTGATTTT
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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 8 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Valine leucine and isoleucine biosynthesis kegg pathway 1.70e-05 1.82e-04 4/52
Metabolic pathways kegg pathway 3.55e-03 1.08e-02 17/52
Biosynthesis of secondary metabolites kegg pathway 3.61e-04 2.17e-03 10/52
Carbohydrate Metabolism kegg subcategory 1.11e-03 6.25e-03 10/52
Amino Acid Metabolism kegg subcategory 5.37e-04 3.38e-03 10/52
Metabolism of Cofactors and Vitamins kegg subcategory 1.39e-03 7.40e-03 6/52
Metabolism kegg subcategory 1.00e-06 1.50e-05 33/52
Metabolism kegg category 6.00e-06 4.40e-05 33/52
Global kegg category 1.00e-06 1.10e-05 33/52
Metabolism kegg category 6.17e-03 1.96e-02 19/52
Carbohydrate Metabolism kegg subcategory 1.85e-02 4.44e-02 5/52
Amino Acid Metabolism kegg subcategory 3.47e-04 2.37e-03 9/52
Valine leucine and isoleucine biosynthesis kegg pathway 1.70e-05 1.92e-04 4/52
Metabolism of Cofactors and Vitamins kegg subcategory 1.39e-03 7.02e-03 6/52
Global kegg category 2.40e-03 1.03e-02 18/52
Metabolism kegg subcategory 2.40e-03 1.03e-02 18/52
Metabolic pathways kegg pathway 3.55e-03 1.33e-02 17/52
Biosynthesis of secondary metabolites kegg pathway 3.61e-04 2.43e-03 10/52

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
thiamine biosynthetic process biological_process 1.56e-04 6.34e-04 3/52
amino acid binding molecular_function 5.50e-05 1.95e-04 3/52
NAD binding molecular_function 1.56e-04 4.80e-04 3/52

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
tRNA aminoacylation tigr sub1role 3.45e-03 6.76e-03 3/52
Energy metabolism tigr mainrole 6.86e-03 2.78e-02 5/52
Protein synthesis tigr mainrole 1.04e-02 3.50e-02 5/52
Amino acid biosynthesis tigr mainrole 3.02e-03 1.74e-02 4/52
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 4.47e-03 2.20e-02 4/52
Energy metabolism tigr mainrole 6.86e-03 9.67e-03 5/52
Protein synthesis tigr mainrole 1.04e-02 1.39e-02 5/52
tRNA aminoacylation tigr sub1role 3.45e-03 5.22e-03 3/52
Amino acid biosynthesis tigr mainrole 3.02e-03 4.64e-03 4/52
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 4.47e-03 6.59e-03 4/52

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 2.04e-02 3.03e-02 8/52
Amino acid transport and metabolism cog subcategory 2.37e-02 3.49e-02 7/52
Coenzyme transport and metabolism cog subcategory 3.15e-02 4.56e-02 6/52
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 8

There are 52 genes in Module 8

Gene Member Table (52)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0025 CDS 2762771 chromosome 32916 33188 - hypothetical protein MMP0025 False
MMP0059 CDS 2762070 chromosome 73629 74051 - hypothetical protein MMP0059 False
MMP0061 aIF6 CDS 2761071 chromosome 74409 75092 - translation initiation factor IF-6 False
MMP0093 CDS 2762081 chromosome 102895 103188 - 50S ribosomal protein L21e False
MMP0094 CDS 2762058 chromosome 103274 104686 - putative pseudouridylate synthase False
MMP0103 CDS 2761393 chromosome 111821 112720 + pyridoxal biosynthesis lyase PdxS False
MMP0116 argC CDS 2761790 chromosome 124154 125185 + N-acetyl-gamma-glutamyl-phosphate reductase False
MMP0127 hmd CDS 2761547 chromosome 133625 134689 - H(2)-dependent methylenetetrahydromethanopterin dehydrogenase False
MMP0183 ribB CDS 2761081 chromosome 192407 193150 - 3,4-dihydroxy-2-butanone 4-phosphate synthase False
MMP0242 CDS 2761651 chromosome 248102 248371 - hypothetical protein MMP0242 False
MMP0290 nac CDS 2761263 chromosome 291206 291586 + nascent polypeptide-associated complex protein False
MMP0309 CDS 2761899 chromosome 306194 306538 + DsrE family protein False
MMP0371 CDS 2761542 chromosome 368523 369152 + hypothetical protein MMP0371 False
MMP0382 CDS 2761707 chromosome 379591 381363 + putative ATPase RIL False
MMP0407 CDS 2762031 chromosome 406129 406542 - hypothetical protein MMP0407 False
MMP0414 thrS CDS 2762044 chromosome 414091 415959 - threonyl-tRNA synthetase False
MMP0539 leuB CDS 2761734 chromosome 543913 544905 + multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase False
MMP0540 purC CDS 2761961 chromosome 545004 545744 + phosphoribosylaminoimidazole-succinocarboxamide synthase False
MMP0597 flpA CDS 2761664 chromosome 593316 594008 + fibrillarin False
MMP0629 CDS 2761638 chromosome 620746 621144 + hypothetical protein MMP0629 True
MMP0645 mdh CDS 2761222 chromosome 636877 637821 - malate dehydrogenase False
MMP0650 ilvB CDS 2761050 chromosome 641377 643140 + acetolactate synthase catalytic subunit False
MMP0651 ilvH CDS 2762012 chromosome 643154 643663 + acetolactate synthase 3 regulatory subunit False
MMP0657 CDS 2761090 chromosome 647675 647947 - hypothetical protein MMP0657 False
MMP0687 tpiA CDS 2762368 chromosome 675181 675702 + triosephosphate isomerase False
MMP0697 leuS CDS 2761186 chromosome 686587 689454 + leucyl-tRNA synthetase False
MMP0704 CDS 2761227 chromosome 694408 695277 - ParA type ATPase False
MMP0736 CDS 2761087 chromosome 729123 729377 + PRC-barrel domain-containing protein False
MMP0737 CDS 2761445 chromosome 729402 730205 + L-aspartate dehydrogenase False
MMP0816 CDS 2761211 chromosome 811265 811486 - seryl-tRNA synthetase-like protein False
MMP0898 CDS 2761860 chromosome 891545 894625 - cellulose-binding protein False
MMP0946 gatB CDS 2761529 chromosome 933286 934695 - aspartyl/glutamyl-tRNA amidotransferase subunit B False
MMP0965 CDS 2762189 chromosome 952509 953087 - formylmethanofuran dehydrogenase subunit E-like protein False
MMP0971 purB CDS 2761379 chromosome 958096 959445 + adenylosuccinate lyase False
MMP1021 CDS 2762795 chromosome 1009427 1010998 - hypothetical protein MMP1021 False
MMP1023 CDS 2761546 chromosome 1012241 1012843 - TetR family transcriptional regulator True
MMP1070 CDS 2761463 chromosome 1062398 1063030 - hypothetical protein MMP1070 False
MMP1213 CDS 2761718 chromosome 1200340 1200732 + hypothetical protein MMP1213 False
MMP1308 tal CDS 2762583 chromosome 1294684 1295331 - putative translaldolase False
MMP1321 rps11p CDS 2762135 chromosome 1306924 1307298 + 30S ribosomal protein S11P False
MMP1352 CDS 2762463 chromosome 1331721 1332509 - ribulose-1,5-biphosphate synthetase False
MMP1512 alr CDS 2761062 chromosome 1470522 1471643 - alanine racemase False
MMP1513 ald CDS 2762318 chromosome 1471700 1472821 - alanine dehydrogenase False
MMP1527 CDS 2761821 chromosome 1486064 1487314 - aspartate aminotransferase False
MMP1531 CDS 2762604 chromosome 1489235 1490206 - hypothetical protein MMP1531 False
MMP1588 serA CDS 2761474 chromosome 1536504 1538075 - D-3-phosphoglycerate dehydrogenase False
MMP1656 CDS 2761526 chromosome 1600220 1600783 - glutamine amidotransferase subunit PdxT False
MMP1698 CDS 2761628 chromosome 1639662 1640198 + hypothetical protein MMP1698 False
MMP1705 CDS 2762448 chromosome 1645566 1646231 - creatininase False
Unanno_15 novel None chromosome 299140 299264 - None False
Unanno_17 novel None chromosome 372862 372930 - None False
Unanno_8 novel None chromosome 141374 141436 - 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 8

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.