Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 13 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 13

There are 0 regulatory influences for Module 13

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
1559 6.70e+04 gcagAgaTTg
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1560 8.00e+04 aACtCGaTcAActgaAaccC
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1561 9.80e+04 aAattcTctgAaTttA.aTTa
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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 13 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nucleotide Metabolism kegg subcategory 9.34e-03 4.22e-02 4/34

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Defense mechanisms cog subcategory 6.18e-04 1.82e-02 3/34
Cellular processes and signaling cog category 2.79e-02 4.47e-02 9/34
Defense mechanisms cog subcategory 6.18e-04 1.24e-03 3/34
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 13

There are 34 genes in Module 13

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0100 CDS 3773440 chromosome 100528 101082 - hypothetical protein False
Synpcc7942_0263 CDS 3773825 chromosome 260700 261620 + Protein of unknown function DUF147 False
Synpcc7942_0264 CDS 3773826 chromosome 261617 262372 + Undecaprenyl pyrophosphate synthetase (EC 2.5.1.31) (IMGterm) False
Synpcc7942_0378 CDS 3774899 chromosome 372532 373326 + Protein of unknown function DUF140 False
Synpcc7942_0380 CDS 3774901 chromosome 373785 374828 + hypothetical protein False
Synpcc7942_0482 CDS 3774720 chromosome 467004 468773 - Peptidoglycan glycosyltransferase (EC:2.4.1.129) False
Synpcc7942_0483 CDS 3774721 chromosome 468776 469219 - hypothetical protein False
Synpcc7942_0577 CDS 3774815 chromosome 558144 558314 + hypothetical protein False
Synpcc7942_0790 CDS 3775967 chromosome 785282 785710 - RNA-binding region RNP-1 False
Synpcc7942_0844 CDS 3774021 chromosome 839099 839809 - Phosphoesterase PHP-like False
Synpcc7942_0971 CDS 3775359 chromosome 977903 979261 - hypothetical protein False
Synpcc7942_1014 CDS 3773942 chromosome 1025629 1028415 - CheA signal transduction histidine kinase (IMGterm) False
Synpcc7942_1072 CDS 3774005 chromosome 1083771 1084322 - "cob(I)yrinic acid a,c-diamide adenosyltransferase (EC 2.5.1.17) (IMGterm)" False
Synpcc7942_1223 CDS 3773511 chromosome 1243830 1245008 - DevC protein False
Synpcc7942_1224 CDS 3773512 chromosome 1244992 1246092 - ABC-transporter membrane fusion protein False
Synpcc7942_1338 CDS 3775531 chromosome 1372863 1373645 - hypothetical protein False
Synpcc7942_1368 CDS 3775562 chromosome 1406657 1406992 + hypothetical protein False
Synpcc7942_1609 CDS 3775676 chromosome 1675456 1678869 + Protein splicing (intein) site (EC:1.17.4.1) False
Synpcc7942_1720 CDS 3775420 chromosome 1791952 1792392 + hypothetical protein False
Synpcc7942_1730 CDS 3775430 chromosome 1802050 1802640 + hypothetical protein False
Synpcc7942_1748 CDS 3775448 chromosome 1818990 1819751 - hypothetical protein False
Synpcc7942_1806 CDS 3774381 chromosome 1875268 1875741 + bacterioferritin comigratory protein (EC:1.11.1.15) False
Synpcc7942_1818 CDS 3774393 chromosome 1891891 1892208 - hypothetical protein False
Synpcc7942_1833 CDS 3774408 chromosome 1901772 1902530 + hypothetical protein False
Synpcc7942_1936 CDS 3775299 chromosome 2010026 2010268 - hypothetical protein False
Synpcc7942_2007 coaD CDS 3774194 chromosome 2075281 2075781 - Phosphopantetheine adenylyltransferase (EC 2.7.7.3) (IMGterm) False
Synpcc7942_2138 CDS 3773695 chromosome 2221934 2222959 + hypothetical protein False
Synpcc7942_2199 CDS 3773756 chromosome 2277916 2280528 - "DNA polymerase III, alpha subunit (EC 2.7.7.7) / intein (IMGterm)" False
Synpcc7942_2202 CDS 3773759 chromosome 2282672 2283169 + HNH nuclease False
Synpcc7942_2294 CDS 3774577 chromosome 2364152 2364988 + hypothetical protein False
Synpcc7942_2403 CDS 3774687 chromosome 2477464 2477748 + hypothetical protein False
Synpcc7942_2404 CDS 3774688 chromosome 2477807 2478547 + hypothetical protein False
Synpcc7942_2427 CDS 3774711 chromosome 2498972 2499814 + "3-mercaptopyruvate sulfurtransferase (EC:2.8.1.1, EC:2.8.1.2)" False
Synpcc7942_2488 CDS 3774508 chromosome 2568903 2569511 + hypothetical protein 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 13

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.