Organism : Methanococcus maripaludis S2 | Module List:
Module 70 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 70

There are 3 regulatory influences for Module 70

Regulator Table (3)
Regulator Name Type
MMP0033
H2		 combiner
MMP0568
H2		 combiner
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
801 1.50e+02 AGAtATgt.gT.gtaAaAACA
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802 4.00e+03 cCgGtaaAAAAgTtTCCgAA
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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 70 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Cofactors and Vitamins kegg subcategory 1.77e-03 8.81e-03 5/40
Metabolism of Cofactors and Vitamins kegg subcategory 1.77e-03 8.31e-03 5/40

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
regulation of transcription, DNA-dependent biological_process 9.74e-03 1.32e-02 3/40
sequence-specific DNA binding transcription factor activity molecular_function 1.84e-03 3.39e-03 3/40
ATP binding molecular_function 6.67e-03 1.00e-02 7/40
ATPase activity molecular_function 6.93e-04 1.55e-03 3/40
iron-sulfur cluster binding molecular_function 2.83e-02 3.55e-02 4/40

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 1.37e-03 1.13e-02 4/40
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 1.37e-03 2.28e-03 4/40

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
General function prediction only cog subcategory 5.20e-05 1.26e-03 12/40
Poorly characterized cog category 1.60e-05 2.63e-04 19/40
Poorly characterized cog category 1.60e-05 3.60e-05 19/40
Posttranslational modification, protein turnover, chaperones cog subcategory 2.27e-02 3.35e-02 3/40
General function prediction only cog subcategory 5.20e-05 1.17e-04 12/40
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 70

There are 40 genes in Module 70

Gene Member Table (40)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Antisense_3 novel None chromosome 344972 345212 + None False
MMP0183 ribB CDS 2761081 chromosome 192407 193150 - 3,4-dihydroxy-2-butanone 4-phosphate synthase False
MMP0220 CDS 2762128 chromosome 227364 228833 + Sodium/proline symporter-related False
MMP0270 CDS 2761468 chromosome 270082 270741 - Fe-S cluster domain-containing protein False
MMP0272 CDS 2762174 chromosome 271467 272258 - ABC transporter ATPase False
MMP0273 comA CDS 2761344 chromosome 272277 272984 - phosphosulfolactate synthase False
MMP0274 hypE CDS 2761321 chromosome 273244 274248 + hydrogenase expression/formation protein HypE False
MMP0345 CDS 2761513 chromosome 341597 342424 - hypothetical protein MMP0345 False
MMP0371 CDS 2761542 chromosome 368523 369152 + hypothetical protein MMP0371 False
MMP0382 CDS 2761707 chromosome 379591 381363 + putative ATPase RIL False
MMP0385 pyrH CDS 2761849 chromosome 384368 385045 - uridylate kinase False
MMP0397 alaS CDS 2761467 chromosome 394599 397277 + alanyl-tRNA synthetase False
MMP0398 CDS 2762691 chromosome 397319 398191 + hypothetical protein MMP0398 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
MMP0402 CDS 2761184 chromosome 400715 402076 + hypothetical protein MMP0402 True
MMP0448 CDS 2762347 chromosome 442923 443207 - hypothetical protein MMP0448 False
MMP0449 CDS 2761658 chromosome 443364 444209 - ferredoxin False
MMP0450 CDS 2761659 chromosome 444206 445063 - ferredoxin False
MMP0451 CDS 2761665 chromosome 445073 445432 - hypothetical protein MMP0451 False
MMP0498 CDS 2761885 chromosome 502095 502658 + hypothetical protein MMP0498 False
MMP0500 CDS 2761396 chromosome 503825 504376 + Iron-sulfur flavoprotein-like protein False
MMP0618 CDS 2761307 chromosome 613463 613792 + hypothetical protein MMP0618 False
MMP0619 CDS 2762028 chromosome 613803 614198 + hypothetical protein MMP0619 False
MMP0620 atwA CDS 2761129 chromosome 614221 615816 + methyl coenzyme M reductase, component A2 False
MMP0816 CDS 2761211 chromosome 811265 811486 - seryl-tRNA synthetase-like protein False
MMP0898 CDS 2761860 chromosome 891545 894625 - cellulose-binding protein False
MMP0899 CDS 2762280 chromosome 894927 895586 + ATP/GTP-binding motif-containing protein False
MMP0900 CDS 2761831 chromosome 895596 896249 + rhodanese domain-containing protein False
MMP0904 selD CDS 2761866 chromosome 898296 899204 - selenophosphate synthetase False
MMP0949 CDS 2761506 chromosome 936440 937774 + tRNA CCA-pyrophosphorylase False
MMP0954 CDS 2761740 chromosome 941822 942295 - hypothetical protein MMP0954 False
MMP0966 cobA CDS 2761559 chromosome 953174 953893 - uroporphyrin-III C-methyltransferase False
MMP1022 CDS 2761270 chromosome 1010991 1012157 - hypothetical protein MMP1022 False
MMP1089 CDS 2762686 chromosome 1081000 1082508 - polysaccharide biosynthesis protein False
MMP1093 coaD CDS 2762207 chromosome 1085368 1085814 - phosphopantetheine adenylyltransferase 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

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.