Organism : Methanococcus maripaludis S2 | Module List:
Module 21 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 21

There are 3 regulatory influences for Module 21

Regulator Table (3)
Regulator Name Type
H2 ef
MMP0036
H2
combiner
MMP1100 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
703 3.80e+03 GGCGaGgc
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704 3.50e+03 CgatTccccCc
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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 21 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 1.25e-03 6.95e-03 7/33
Amino Acid Metabolism kegg subcategory 7.64e-03 2.31e-02 5/33

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
regulation of transcription, DNA-dependent biological_process 4.86e-03 7.56e-03 3/33
ATP binding molecular_function 1.86e-03 3.41e-03 7/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 2.29e-02 2.82e-02 3/33
Protein synthesis tigr mainrole 3.04e-02 3.63e-02 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 1.33e-03 1.40e-02 7/33
Information storage and processing cog category 1.03e-02 1.58e-02 9/33
Transcription cog subcategory 2.16e-02 3.19e-02 3/33
Amino acid transport and metabolism cog subcategory 1.33e-03 2.22e-03 7/33
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 21

There are 33 genes in Module 21

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
MMP0228 trm1 CDS 2762025 chromosome 236852 237973 + N(2),N(2)-dimethylguanosine tRNA methyltransferase False
MMP0270 CDS 2761468 chromosome 270082 270741 - Fe-S cluster domain-containing protein False
MMP0271 CDS 2762176 chromosome 270743 271441 - putative ATP binding nickel incorporation protein False
MMP0272 CDS 2762174 chromosome 271467 272258 - ABC transporter ATPase False
MMP0273 comA CDS 2761344 chromosome 272277 272984 - phosphosulfolactate synthase 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
MMP0698 CDS 2761992 chromosome 689482 689799 + hypothetical protein MMP0698 False
MMP0904 selD CDS 2761866 chromosome 898296 899204 - selenophosphate synthetase False
MMP0954 CDS 2761740 chromosome 941822 942295 - hypothetical protein MMP0954 False
MMP1021 CDS 2762795 chromosome 1009427 1010998 - hypothetical protein MMP1021 False
MMP1022 CDS 2761270 chromosome 1010991 1012157 - hypothetical protein MMP1022 False
MMP1023 CDS 2761546 chromosome 1012241 1012843 - TetR family transcriptional regulator True
MMP1026 argS CDS 2761358 chromosome 1015747 1017447 - arginyl-tRNA synthetase False
MMP1186 lon CDS 2761190 chromosome 1168587 1170665 + thiol (cysteine) protease False
MMP1200 lysA CDS 2761645 chromosome 1186534 1187844 + diaminopimelate decarboxylase False
MMP1259 CDS 2762620 chromosome 1242092 1243420 - FAD-dependent pyridine nucleotide-disulfide oxidoreductase False
MMP1317 CDS 2762707 chromosome 1302557 1303333 - hypothetical protein MMP1317 False
MMP1318 lysS CDS 2761127 chromosome 1303479 1305104 - lysyl-tRNA synthetase False
MMP1358 CDS 2762433 chromosome 1336828 1337226 - ferredoxin 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
MMP1583 CDS 2761958 chromosome 1533600 1533968 + S-adenosylmethionine decarboxylase-like protein False
MMP1584 CDS 2761959 chromosome 1533965 1534807 + spermidine synthase False
MMP1611 CDS 2761575 chromosome 1557924 1558676 - hypothetical protein MMP1611 False
MMP1657 CDS 2761355 chromosome 1601691 1602863 + hypothetical protein MMP1657 False
MMP1681 CDS 2762658 chromosome 1622934 1624220 - hypothetical protein MMP1681 False
MMP1682 recJ CDS 2761922 chromosome 1624270 1625673 - single stranded DNA-specific exonuclease False
MMP1704 CDS 2762447 chromosome 1645101 1645556 - hypothetical protein MMP1704 True
MMP1706 CDS 2761368 chromosome 1646237 1646392 - H/ACA RNA-protein complex component Nop10p False
MMP1707 aIF2_alpha CDS 2761369 chromosome 1646401 1647198 - translation initiation factor IF-2 subunit alpha 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 21

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.