Organism : Methanococcus maripaludis S2 | Module List:
Module 78 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 78

There are 8 regulatory influences for Module 78

Regulator Table (8)
Regulator Name Type
MMP1304 tf
MMP1704 tf
MMP0031
H2		 combiner
MMP0052
MMP1304		 combiner
MMP0033 tf
MMP0840
H2		 combiner
MMP1052 tf
MMP0465
Formate		 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
817 1.30e+00 GTTTT.A.CaGCac
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818 9.50e+02 gtATAacgtaTA.aTataGGTagg
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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 78 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Folding Sorting and Degradation kegg subcategory 2.25e-04 1.56e-03 3/27
Nucleotide Metabolism kegg subcategory 1.71e-02 4.21e-02 3/27
Folding Sorting and Degradation kegg subcategory 2.25e-04 1.75e-03 3/27

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
thiamine biosynthetic process biological_process 1.10e-05 5.70e-05 3/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Thiamine tigr sub1role 0.00e+00 4.00e-06 3/27
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 7.54e-04 8.41e-03 3/27
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 2.29e-03 1.49e-02 3/27
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 7.54e-04 1.34e-03 3/27
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 2.29e-03 3.62e-03 3/27
Thiamine tigr sub1role 0.00e+00 1.00e-06 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 5.67e-03 3.99e-02 3/27
Nucleotide transport and metabolism cog subcategory 6.61e-03 4.42e-02 3/27
Cellular processes and signaling cog category 3.03e-02 4.39e-02 5/27
Transcription cog subcategory 1.07e-02 1.63e-02 3/27
Posttranslational modification, protein turnover, chaperones cog subcategory 5.67e-03 8.84e-03 3/27
Amino acid transport and metabolism cog subcategory 3.44e-02 4.95e-02 4/27
Nucleotide transport and metabolism cog subcategory 6.61e-03 1.03e-02 3/27
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 78

There are 27 genes in Module 78

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0290 nac CDS 2761263 chromosome 291206 291586 + nascent polypeptide-associated complex protein False
MMP0308 CDS 2761386 chromosome 305972 306184 + SirA family protein False
MMP0309 CDS 2761899 chromosome 306194 306538 + DsrE family protein False
MMP0355 CDS 2761907 chromosome 351015 352514 - hypothetical protein MMP0355 False
MMP0359 CDS 2761116 chromosome 355921 356598 - glycosyl transferase family protein False
MMP0377 CDS 2762681 chromosome 374200 374844 - isoleucyl-tRNA synthetase-like protein False
MMP0381 CDS 2762505 chromosome 379027 379512 + 3-isopropylmalate dehydratase small subunit False
MMP0382 CDS 2761707 chromosome 379591 381363 + putative ATPase RIL False
MMP0385 pyrH CDS 2761849 chromosome 384368 385045 - uridylate kinase False
MMP0391 aspC CDS 2762733 chromosome 388479 389627 - aspartate aminotransferase False
MMP0396 eno CDS 2761376 chromosome 393105 394397 + phosphopyruvate hydratase False
MMP0397 alaS CDS 2761467 chromosome 394599 397277 + alanyl-tRNA synthetase False
MMP0399 htpX CDS 2762520 chromosome 398202 399059 + heat shock protein HtpX False
MMP0400 ehbQ CDS 2761054 chromosome 399069 399722 + amino acid-binding ACT domain-containing protein False
MMP0410 prsA CDS 2762426 chromosome 408933 409796 + ribose-phosphate pyrophosphokinase False
MMP0500 CDS 2761396 chromosome 503825 504376 + Iron-sulfur flavoprotein-like protein False
MMP0704 CDS 2761227 chromosome 694408 695277 - ParA type ATPase False
MMP1023 CDS 2761546 chromosome 1012241 1012843 - TetR family transcriptional regulator True
MMP1116 CDS 2761521 chromosome 1106057 1107109 + cellulase False
MMP1129 ppiB CDS 2762628 chromosome 1119759 1120247 - cyclophilin type peptidyl-prolyl cis-trans isomerase False
MMP1137 CDS 2762104 chromosome 1127432 1127854 - Lrp/AsnC family transcriptional regulator True
MMP1138 thiM CDS 2762053 chromosome 1128004 1128864 + hydroxyethylthiazole kinase False
MMP1139 thiE CDS 2762052 chromosome 1128854 1129477 + thiamine-phosphate pyrophosphorylase False
MMP1352 CDS 2762463 chromosome 1331721 1332509 - ribulose-1,5-biphosphate synthetase False
MMP1589 carA CDS 2761796 chromosome 1538219 1539319 + carbamoyl phosphate synthase small subunit False
Unanno_33 novel None chromosome 562667 562747 + 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.

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.