Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 15 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 15

There are 0 regulatory influences for Module 15

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
1565 7.60e-01 acTcagccaAC.CtagAGtgc
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1566 1.80e+00 atTggctgc.CATGgctAcgatCc
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1567 6.20e+00 CAagt..ccgttgCTtta.cG
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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 15 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
General function prediction only cog subcategory 5.93e-04 1.82e-02 9/33
Poorly characterized cog category 2.06e-03 4.32e-02 11/33
Poorly characterized cog category 2.06e-03 3.84e-03 11/33
Transcription cog subcategory 2.19e-02 3.58e-02 3/33
Inorganic ion transport and metabolism cog subcategory 2.53e-02 4.10e-02 4/33
General function prediction only cog subcategory 5.93e-04 1.20e-03 9/33
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 15

There are 33 genes in Module 15

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0036 CDS 3775849 chromosome 35341 36126 + hypothetical protein False
Synpcc7942_0040 CDS 3775752 chromosome 38630 39007 + dihydroneopterin aldolase Dihydroneopterin aldolase (EC:4.1.2.25) False
Synpcc7942_0041 CDS 3775753 chromosome 39441 40745 + possible tyrosine transporter P-protein (TC 2.A.45.2.1) (IMGterm) False
Synpcc7942_0057 CDS 3775770 chromosome 59072 60304 - putative C-3 methyl transferase False
Synpcc7942_0526 CDS 3774764 chromosome 510412 511293 + "carbohydrate ABC transporter membrane protein 1, CUT1 family (TC 3.A.1.1.-) (IMGterm)" False
Synpcc7942_0650 CDS 3775633 chromosome 644174 644659 - hypothetical protein False
Synpcc7942_0651 CDS 3775634 chromosome 644741 647161 + replication restart DNA helicase PriA (IMGterm) False
Synpcc7942_0672 CDS 3775655 chromosome 666887 667849 + group2 RNA polymerase sigma factor SigD True
Synpcc7942_0688 CDS 3775858 chromosome 683722 684060 + "transcriptional regulator, ArsR family (IMGterm)" True
Synpcc7942_0947 CDS 3775335 chromosome 955647 956714 - "carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-) (IMGterm)" False
Synpcc7942_0981 CDS 3775370 chromosome 989800 991494 - hypothetical protein False
Synpcc7942_1034 CDS 3773964 chromosome 1048952 1049815 + Transglutaminase-like False
Synpcc7942_1111 CDS 3775061 chromosome 1127864 1129447 - serine/threonine protein kinase (IMGterm) False
Synpcc7942_1112 CDS 3775062 chromosome 1129444 1130385 - ribosomal large subunit pseudouridine synthase D (EC 5.4.99.-) (IMGterm) False
Synpcc7942_1193 CDS 3774429 chromosome 1221676 1222398 - Phospholipid/glycerol acyltransferase False
Synpcc7942_1299 CDS 3773588 chromosome 1326892 1327854 - hypothetical protein False
Synpcc7942_1371 CDS 3775565 chromosome 1408205 1409368 - magnesium and cobalt transport protein CorA False
Synpcc7942_1558 CDS 3774982 chromosome 1615204 1616271 + hypothetical protein False
Synpcc7942_1575 CDS 3774999 chromosome 1636580 1638625 + Glycogen debranching enzyme False
Synpcc7942_1599 CDS 3775023 chromosome 1665097 1666182 + hypothetical protein False
Synpcc7942_1773 CDS 3774348 chromosome 1839008 1839325 + hypothetical protein False
Synpcc7942_1889 CDS 3775252 chromosome 1961987 1963582 - (1->4)-alpha-D-glucan branching enzyme (IMGterm) False
Synpcc7942_2011 CDS 3774198 chromosome 2080210 2081391 - RNAse Z (EC 3.1.26.11) (IMGterm) False
Synpcc7942_2012 CDS 3774199 chromosome 2081506 2082729 + stage II sporulation protein D-like False
Synpcc7942_2035 CDS 3774254 chromosome 2104481 2105518 - hypothetical protein False
Synpcc7942_2279 CDS 3774561 chromosome 2347614 2349026 + ammonium transporter (TC 1.A.11) (IMGterm) False
Synpcc7942_2303 CDS 3774586 chromosome 2371417 2372253 + Dihydropteroate synthase (EC 2.5.1.15) (IMGterm) False
Synpcc7942_2311 CDS 3774594 chromosome 2379602 2380381 - hypothetical protein False
Synpcc7942_2328 CDS 3774611 chromosome 2394836 2395927 + TPR repeat False
Synpcc7942_2329 CDS 3774612 chromosome 2395924 2397198 - metal dependent phosphohydrolase (IMGterm) False
Synpcc7942_2594 CDS 3775191 chromosome 2676760 2677371 + hypothetical protein False
Synpcc7942_2595 CDS 3775192 chromosome 2677378 2678808 + hypothetical protein False
Synpcc7942_2596 CDS 3775193 chromosome 2678860 2679921 + probable oxidoreductase 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 15

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.