Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 59 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 59

There are 0 regulatory influences for Module 59

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
1697 3.50e+01 tCgGCccTGTCatcgagGaTg
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1698 1.50e+02 AaTataaaaaGagTTtgGCAGaCt
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1699 5.70e+02 AtTtGacGAcacaGtttaaGaTGA
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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 59 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Lipid Metabolism kegg subcategory 7.00e-06 1.64e-04 4/21
Amino Acid Metabolism kegg subcategory 8.27e-03 3.89e-02 4/21
Metabolism kegg subcategory 0.00e+00 0.00e+00 20/21
Metabolism kegg category 5.40e-05 6.97e-04 16/21
Global kegg category 0.00e+00 0.00e+00 20/21
Metabolism kegg category 2.18e-04 3.15e-03 12/21
Lipid Metabolism kegg subcategory 7.60e-05 1.62e-03 3/21
Amino Acid Metabolism kegg subcategory 2.25e-03 1.25e-02 4/21
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 9.00e-06 3.21e-04 3/21
Global kegg category 5.20e-05 1.29e-03 12/21
Metabolism kegg subcategory 5.20e-05 1.29e-03 12/21
Metabolic pathways kegg pathway 3.70e-05 1.00e-03 12/21
Biosynthesis of secondary metabolites kegg pathway 1.16e-04 2.15e-03 7/21

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis tigr sub1role 6.00e-06 1.25e-04 3/21
Fatty acid and phospholipid metabolism tigr mainrole 6.00e-06 3.29e-04 3/21
Amino acid biosynthesis tigr mainrole 4.06e-04 8.79e-03 3/21
Fatty acid and phospholipid metabolism tigr mainrole 6.00e-06 1.80e-05 3/21
Biosynthesis tigr sub1role 6.00e-06 1.80e-05 3/21
Amino acid biosynthesis tigr mainrole 4.06e-04 8.57e-04 3/21

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Lipid transport and metabolism cog subcategory 6.01e-04 1.82e-02 3/21
Metabolism cog category 1.88e-02 3.10e-02 10/21
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
Lipid transport and metabolism cog subcategory 6.01e-04 1.21e-03 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 59

There are 21 genes in Module 59

Gene Member Table (21)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0077 CDS 3773794 chromosome 75928 76617 + "transcriptional regulator, XRE family (IMGterm)" False
Synpcc7942_0231 CDS 3775839 chromosome 227407 227931 - putative acetyltransferase False
Synpcc7942_0232 CDS 3775840 chromosome 227939 229285 - 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (IMGterm) False
Synpcc7942_0393 CDS 3774914 chromosome 386677 387357 + hypothetical protein False
Synpcc7942_0652 CDS 3775635 chromosome 647124 648713 - hypothetical protein False
Synpcc7942_0894 aroK CDS 3774072 chromosome 904845 905417 - shikimate kinase (EC 2.7.1.71) (IMGterm) False
Synpcc7942_0896 CDS 3774074 chromosome 906832 907638 + septum site-determining protein MinD (IMGterm) False
Synpcc7942_0897 CDS 3774075 chromosome 907653 907928 + cell division topological specificity factor MinE (IMGterm) False
Synpcc7942_0994 CDS 3773921 chromosome 1003177 1003746 - hypothetical protein False
Synpcc7942_1378 CDS 3775572 chromosome 1419926 1421167 - hypothetical protein (EC:2.4.1.182) False
Synpcc7942_1379 CDS 3775573 chromosome 1421475 1422836 + acetyl-CoA carboxylase carboxyltransferase subunit alpha / biotin carboxylase (EC 6.3.4.14) (IMGterm) False
Synpcc7942_1428 CDS 3773600 chromosome 1481407 1482594 + 5-(carboxyamino)imidazole ribonucleotide synthase (IMGterm) False
Synpcc7942_1455 CDS 3773627 chromosome 1508394 1509401 + 3-oxoacyl-[acyl-carrier-protein] synthase III (EC 2.3.1.41) (IMGterm) False
Synpcc7942_1457 CDS 3773629 chromosome 1510305 1510982 + 1-acyl-sn-glycerol-3-phosphate acyltransferase (EC 2.3.1.51) (IMGterm) False
Synpcc7942_1500 prmA CDS 3773673 chromosome 1549179 1550078 - [LSU ribosomal protein L11P]-lysine N-methyltransferase (EC 2.1.1.-) (IMGterm) False
Synpcc7942_1910 CDS 3775273 chromosome 1985741 1986379 - 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (EC:4.1.1.-) False
Synpcc7942_1992 CDS 3774179 chromosome 2062388 2063434 - methylthioribose-1-phosphate isomerase (EC 5.3.1.23) (IMGterm) False
Synpcc7942_2085 CDS 3774304 chromosome 2165683 2166759 - arsenite efflux ATP-binding protein ArsA (TC 3.A.4.1.1) (IMGterm) False
Synpcc7942_2123 trpD CDS 3774342 chromosome 2203801 2204847 - anthranilate phosphoribosyltransferase (EC 2.4.2.18) (IMGterm) False
Synpcc7942_2569 CDS 3775162 chromosome 2648098 2648820 - orotidine-5'-phosphate decarboxylase (EC 4.1.1.23) (IMGterm) False
Synpcc7942_2570 CDS 3775163 chromosome 2648824 2650032 - tyrosyl-tRNA synthetase (EC 6.1.1.1) (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.