Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 186 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 186

There are 0 regulatory influences for Module 186

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
2075 9.20e-01 cgccAGaaactGGtcgaaGagCag
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2076 1.80e+00 CgcTTcaGG.CtTg.CatCCC
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2077 4.60e+02 CAaacCTgTtaGgacAGACtA
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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 186 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Folding Sorting and Degradation kegg subcategory 7.18e-04 7.80e-03 3/27
Membrane Transport kegg subcategory 6.03e-03 3.26e-02 3/27
Folding Sorting and Degradation kegg subcategory 7.18e-04 6.69e-03 3/27
RNA degradation kegg pathway 2.50e-05 7.72e-04 3/27
Membrane Transport kegg subcategory 6.03e-03 2.03e-02 3/27
ABC transporters kegg pathway 3.34e-03 1.54e-02 3/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Anions tigr sub1role 4.30e-05 6.29e-04 3/27
Transport and binding proteins tigr mainrole 1.34e-03 1.80e-02 3/27
Transport and binding proteins tigr mainrole 1.34e-03 2.50e-03 3/27
Anions tigr sub1role 4.30e-05 1.13e-04 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Inorganic ion transport and metabolism cog subcategory 2.05e-03 3.80e-02 5/27
Cell wall/membrane/envelope biogenesis cog subcategory 2.81e-02 4.49e-02 3/27
Inorganic ion transport and metabolism cog subcategory 2.05e-03 3.81e-03 5/27
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 186

There are 27 genes in Module 186

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0019 CDS 3774239 chromosome 18615 20489 + sulfite reductase (ferredoxin) (EC 1.8.7.1) (IMGterm) False
Synpcc7942_0347 CDS 3774868 chromosome 340288 340452 + hypothetical protein False
Synpcc7942_0394 CDS 3774915 chromosome 387354 388220 - phosphatidate cytidylyltransferase (EC:2.7.7.41) False
Synpcc7942_0708 CDS 3775879 chromosome 698708 700459 + hypothetical protein False
Synpcc7942_0715 CDS 3775886 chromosome 709992 711179 + UDP-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7) (IMGterm) False
Synpcc7942_0861 CDS 3774038 chromosome 864180 865469 - hypothetical protein False
Synpcc7942_0864 CDS 3774041 chromosome 867395 867913 + hypothetical protein False
Synpcc7942_0878 CDS 3774055 chromosome 883835 886261 + "ribonuclease, Rne/Rng family (EC:3.1.26.12)" False
Synpcc7942_0928 CDS 3774927 chromosome 934864 937029 + outer envelope membrane protein False
Synpcc7942_0929 lpxC CDS 3774928 chromosome 937039 937893 + UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase (EC 3.5.1.-) (IMGterm) False
Synpcc7942_1032 CDS 3773962 chromosome 1046506 1047972 + hypothetical protein False
Synpcc7942_1033 CDS 3773963 chromosome 1047992 1048948 + hypothetical protein False
Synpcc7942_1105 CDS 3775055 chromosome 1122449 1123534 - MRP protein-like False
Synpcc7942_1287 CDS 3773576 chromosome 1309030 1310862 + VCBS False
Synpcc7942_1373 CDS 3775567 chromosome 1413287 1413982 - hydrogenase accessory protein False
Synpcc7942_1680 CDS 3775216 chromosome 1747842 1748858 - Sulphate transport system permease protein 1 (EC:3.6.3.25) False
Synpcc7942_1681 CDS 3775380 chromosome 1749076 1750128 + Thiosulphate-binding protein False
Synpcc7942_1683 CDS 3775382 chromosome 1751063 1751308 + hypothetical protein False
Synpcc7942_1684 CDS 3775383 chromosome 1751336 1751956 + "putative transcriptional regulator, Crp/Fnr family" True
Synpcc7942_1685 CDS 3775384 chromosome 1752002 1752862 + Sulphate transport system permease protein 2 False
Synpcc7942_1846 CDS 3774421 chromosome 1911978 1913807 - hypothetical protein (EC:3.1.-) False
Synpcc7942_1883 CDS 3775246 chromosome 1955407 1956126 - conserved hypothetical protein YCF53 False
Synpcc7942_1911 CDS 3775274 chromosome 1986376 1988613 - RNAse R (EC 3.1.-.-) (IMGterm) True
Synpcc7942_2454 CDS 3774473 chromosome 2532100 2533374 - adenine phosphoribosyltransferase (EC 2.4.2.7) (IMGterm) False
Synpcc7942_2455 CDS 3774474 chromosome 2533536 2534168 + hypothetical protein False
Synpcc7942_2488 CDS 3774508 chromosome 2568903 2569511 + hypothetical protein False
Synpcc7942_2589 CDS 3775186 chromosome 2673063 2673848 + 2-phosphosulfolactate phosphatase (EC 3.1.3.71) (IMGterm) 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 186

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.