Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 66 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 66

There are 0 regulatory influences for Module 66

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
1718 5.10e+03 a.cAaTa.CaatG.cAaAaaa
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1719 1.00e+05 TTgtCCcGaTcattGTctG
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1720 1.50e+05 AAGTTTCTGAGA
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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 66 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 2.35e-03 1.82e-02 4/25
Translation kegg subcategory 7.86e-04 8.13e-03 4/25
Replication and Repair kegg subcategory 6.39e-03 3.38e-02 3/25
Genetic Information Processing kegg category 6.87e-04 6.31e-03 7/25
Genetic Information Processing kegg category 7.05e-03 2.26e-02 5/25
Translation kegg subcategory 7.86e-04 7.04e-03 4/25
Ribosome kegg pathway 2.55e-04 3.53e-03 4/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Ribosomal proteins: synthesis and modification tigr sub1role 1.56e-03 4.04e-03 3/25
Protein synthesis tigr mainrole 2.24e-02 2.82e-02 3/25
Ribosomal proteins: synthesis and modification tigr sub1role 1.56e-03 2.86e-03 3/25

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 66

There are 25 genes in Module 66

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0001 CDS 3774221 chromosome 65 1237 + "DNA polymerase III, beta subunit (EC 2.7.7.7) (IMGterm)" False
Synpcc7942_0137 hemH CDS 3773477 chromosome 138115 139278 + ferrochelatase (EC 4.99.1.1) (IMGterm) 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_0446 rpsN CDS 3773391 chromosome 436519 436821 - SSU ribosomal protein S14P (IMGterm) False
Synpcc7942_0457 CDS 3773403 chromosome 445562 446179 + hypothetical protein False
Synpcc7942_0690 clpS CDS 3775860 chromosome 684868 685155 - hypothetical protein False
Synpcc7942_0773 CDS 3775950 chromosome 765592 766197 - conserved hypothetical protein YCF52 False
Synpcc7942_0790 CDS 3775967 chromosome 785282 785710 - RNA-binding region RNP-1 False
Synpcc7942_0882 CDS 3774059 chromosome 888440 889096 - "Peptidase S16, lon-like (EC:3.4.21.53)" False
Synpcc7942_0918 CDS 3774096 chromosome 924079 926028 + long-chain-fatty-acid CoA ligase (EC:6.2.1.3) False
Synpcc7942_0919 CDS 3774097 chromosome 926077 926523 + hypothetical protein False
Synpcc7942_1152 CDS 3775102 chromosome 1177670 1178677 - rare lipoprotein A False
Synpcc7942_1220 rpmA CDS 3773508 chromosome 1242067 1242333 + LSU ribosomal protein L27P (IMGterm) False
Synpcc7942_1439 CDS 3773611 chromosome 1492429 1494030 - NADH dehydrogenase subunit M (EC 1.6.5.3) (IMGterm) True
Synpcc7942_1609 CDS 3775676 chromosome 1675456 1678869 + Protein splicing (intein) site (EC:1.17.4.1) False
Synpcc7942_1730 CDS 3775430 chromosome 1802050 1802640 + hypothetical protein False
Synpcc7942_1749 CDS 3775449 chromosome 1819754 1820146 - ferredoxin False
Synpcc7942_1761 CDS 3775463 chromosome 1827800 1829530 + hypothetical protein False
Synpcc7942_1774 rpsU CDS 3774349 chromosome 1839385 1839558 + SSU ribosomal protein S21P (IMGterm) False
Synpcc7942_2026 CDS 3774213 chromosome 2094451 2095854 + probable glycosyltransferase False
Synpcc7942_2234 CDS 3773890 chromosome 2300183 2300659 + NADH dehydrogenase I subunit N (EC:1.6.5.3) False
Synpcc7942_2249 CDS 3773905 chromosome 2316062 2316487 - adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (IMGterm) False
Synpcc7942_2255 CDS 3773911 chromosome 2325520 2325924 + hypothetical protein False
Synpcc7942_2559 rplI CDS 3775152 chromosome 2637730 2638188 - LSU ribosomal protein L9P (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 66

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.