Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 74 Profile

GeneModule member RegulatorRegulator MotifMotif
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 74

There are 0 regulatory influences for Module 74

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
1742 2.50e+03 Gcccc.acaGcagC.g.acacTcG
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1743 1.40e+04 CTgAGCAa
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1744 7.50e+04 TtGGTCgtTtgcTtttat
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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 74 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 7.91e-03 3.77e-02 3/21
Amino Acid Metabolism kegg subcategory 1.38e-03 1.23e-02 5/21
Metabolism kegg subcategory 2.76e-04 3.50e-03 14/21
Metabolism kegg category 5.40e-05 6.97e-04 16/21
Global kegg category 2.76e-04 2.96e-03 14/21
Metabolism kegg category 4.33e-03 1.74e-02 10/21
Amino Acid Metabolism kegg subcategory 2.25e-03 1.25e-02 4/21
Metabolism of Cofactors and Vitamins kegg subcategory 2.19e-02 4.68e-02 3/21
Global kegg category 1.95e-02 4.34e-02 8/21
Metabolism kegg subcategory 1.95e-02 4.34e-02 8/21
Metabolic pathways kegg pathway 1.59e-02 3.74e-02 8/21
Biosynthesis of secondary metabolites kegg pathway 8.13e-04 7.20e-03 6/21

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 1.22e-02 4.73e-02 3/21
Protein synthesis tigr mainrole 1.22e-02 1.69e-02 3/21

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 3.10e-02 4.91e-02 5/21
Translation, ribosomal structure and biogenesis cog subcategory 2.39e-02 3.87e-02 3/21
Amino acid transport and metabolism cog subcategory 2.67e-02 4.29e-02 3/21
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 74

There are 21 genes in Module 74

Gene Member Table (21)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0101 CDS 3773441 chromosome 101259 102593 + type 2 NADH dehydrogenase (EC:1.6.99.3) False
Synpcc7942_0125 hisB CDS 3773465 chromosome 124738 125367 - imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IMGterm) False
Synpcc7942_0126 CDS 3773466 chromosome 125382 126158 - Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) (IMGterm) False
Synpcc7942_0396 purH CDS 3774917 chromosome 389953 391494 + IMP cyclohydrolase (EC 3.5.4.10) / phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) (IMGterm) False
Synpcc7942_0449 CDS 3773394 chromosome 438675 440006 - seryl-tRNA synthetase (EC 6.1.1.11) (IMGterm) False
Synpcc7942_0618 CDS 3775600 chromosome 607820 609100 + adenosylhomocysteinase (EC 3.3.1.1) (IMGterm) False
Synpcc7942_0626 CDS 3775609 chromosome 618362 620221 + dihydroxyacid dehydratase (EC 4.2.1.9) (IMGterm) False
Synpcc7942_0653 CDS 3775636 chromosome 648710 649441 - Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family-like (EC:5.2.1.8) False
Synpcc7942_0654 CDS 3775637 chromosome 649443 650009 - photosystem I assembly related protein False
Synpcc7942_0678 CDS 3775661 chromosome 672767 673402 + 3'-5' exonuclease (EC:3.1.13.5) False
Synpcc7942_0713 ispG CDS 3775884 chromosome 706450 707673 - 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (EC 1.17.4.3) (IMGterm) False
Synpcc7942_1142 CDS 3775092 chromosome 1166949 1168526 + methionyl-tRNA synthetase (EC 6.1.1.10) (IMGterm) False
Synpcc7942_1496 CDS 3773669 chromosome 1546647 1547552 - N-acetylglutamate kinase (EC 2.7.2.8) (IMGterm) False
Synpcc7942_2044 CDS 3774263 chromosome 2112977 2113990 - hypothetical protein False
Synpcc7942_2063 surE CDS 3774282 chromosome 2139891 2140667 - 5'-nucleotidase (EC 3.1.3.5) / exopolyphosphatase (EC 3.6.1.11) / 3'-nucleotidase (EC 3.1.3.6) (IMGterm) False
Synpcc7942_2067 CDS 3774286 chromosome 2143337 2144584 + hypothetical protein False
Synpcc7942_2470 CDS 3774490 chromosome 2551697 2552464 + hypothetical protein False
Synpcc7942_2471 nusB CDS 3774491 chromosome 2552611 2553252 + transcription antitermination factor NusB True
Synpcc7942_2491 gyrB CDS 3774511 chromosome 2571012 2572949 + DNA gyrase subunit B (EC 5.99.1.3) (IMGterm) False
Synpcc7942_2525 CDS 3775117 chromosome 2606782 2607516 + ATP-dependent Clp protease proteolytic subunit ClpP (EC 3.4.21.92) (IMGterm) False
Synpcc7942_2565 CDS 3775158 chromosome 2644835 2645392 - translation elongation factor P (EF-P) (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.

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.