Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 38 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 38

There are 0 regulatory influences for Module 38

Warning: No Regulators were found!

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 3 motifs predicted.

Motif Table (3)
Motif Id e-value Consensus Motif Logo
1634 2.50e+00 TTGtcaaAgTCTTgGGtCAA
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1635 1.70e+02 AtgtTgtTcaaataaCCTaAGGtA
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1636 1.80e+03 CAGCcTA
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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 38 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 8.37e-03 1.46e-02 4/31
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 38

There are 31 genes in Module 38

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0046 CDS 3775759 chromosome 45164 46507 + Methylase involved in ubiquinone/menaquinone biosynthesis-like False
Synpcc7942_0139 CDS 3773479 chromosome 140268 142106 + "acetolactate synthase, large subunit (EC 2.2.1.6) (IMGterm)" False
Synpcc7942_0236 CDS 3775844 chromosome 232018 232557 + cyclic nucleotide-binding domain (cNMP-BD) protein False
Synpcc7942_0255 CDS 3773818 chromosome 251503 252783 - ATPase False
Synpcc7942_0276 CDS 3773838 chromosome 270001 271473 - glycolate oxidase subunit GlcD (EC:1.1.3.15) False
Synpcc7942_0349 CDS 3774870 chromosome 341883 342443 - hypothetical protein False
Synpcc7942_0360 CDS 3774881 chromosome 353103 354299 - hypothetical protein False
Synpcc7942_0410 CDS 3773355 chromosome 401750 402022 - hypothetical protein False
Synpcc7942_0607 CDS 3775589 chromosome 595381 595707 + hypothetical protein False
Synpcc7942_0608 CDS 3775590 chromosome 595756 596298 + acireductone dioxygenase apoprotein (IMGterm) False
Synpcc7942_0860 CDS 3774037 chromosome 862987 863946 + CheW protein (IMGterm) False
Synpcc7942_0909 CDS 3774087 chromosome 918135 918491 + HesB/YadR/YfhF False
Synpcc7942_1015 CDS 3773943 chromosome 1028418 1030937 - methyl-accepting chemotaxis sensory transducer (IMGterm) False
Synpcc7942_1259 CDS 3773548 chromosome 1281993 1283171 + arsenite efflux ATP-binding protein ArsA (TC 3.A.4.1.1) (IMGterm) False
Synpcc7942_1414 CDS 3774127 chromosome 1465709 1466434 - ATPase False
Synpcc7942_1429 CDS 3773601 chromosome 1482857 1483267 - hypothetical protein False
Synpcc7942_1430 CDS 3773602 chromosome 1483316 1484251 - hypothetical protein False
Synpcc7942_1451 CDS 3773623 chromosome 1504300 1504761 + hypothetical protein False
Synpcc7942_1510 CDS 3774934 chromosome 1560399 1561178 - "RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG (IMGterm)" True
Synpcc7942_1733 CDS 3775433 chromosome 1803575 1804219 - transcriptional regulator (IMGterm) True
Synpcc7942_1837 CDS 3774412 chromosome 1904030 1904374 - hypothetical protein False
Synpcc7942_1951 CDS 3774136 chromosome 2024828 2025190 + hypothetical protein False
Synpcc7942_1986 CDS 3774173 chromosome 2056331 2057653 - "processing protease (EC:3.4.99.-, EC:3.4.24.64)" False
Synpcc7942_2144 CDS 3773701 chromosome 2228529 2229017 - nuclease (SNase-like) (EC:3.1.31.1) False
Synpcc7942_2171 CDS 3773728 chromosome 2252196 2252726 - starvation induced DNA binding protein False
Synpcc7942_2190 CDS 3773747 chromosome 2267935 2268357 + Methionine sulfoxide reductase B (EC:1.8.4.12) False
Synpcc7942_2240 CDS 3773896 chromosome 2305961 2306491 + conserved hypothetical protein YCF52 False
Synpcc7942_2282 CDS 3774564 chromosome 2351102 2353015 - GAF sensor signal transduction histidine kinase (EC 2.7.13.3) (IMGterm) False
Synpcc7942_2420 CDS 3774704 chromosome 2492215 2492949 + serine O-acetyltransferase (EC 2.3.1.30) (IMGterm) False
Synpcc7942_2423 CDS 3774707 chromosome 2494868 2496775 - glucose inhibited division protein A False
Synpcc7942_2480 CDS 3774500 chromosome 2560946 2561848 - "Prolyl 4-hydroxylase, alpha subunit" 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 38

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.