Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 104 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 104

There are 0 regulatory influences for Module 104

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
1832 6.20e+00 Tccaca.cgaTcgCtGcCag.ga
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1833 4.50e+01 GCGacatttggAagt.GacTAtC
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1834 1.20e+03 caGAtTGC
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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 104 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 3.79e-03 2.47e-02 5/21
Metabolism kegg subcategory 0.00e+00 0.00e+00 22/21
Metabolism kegg category 1.00e-06 1.00e-05 18/21
Global kegg category 0.00e+00 0.00e+00 22/21
Metabolism kegg category 1.06e-03 8.33e-03 11/21
Carbohydrate Metabolism kegg subcategory 1.96e-03 1.18e-02 4/21
Metabolism of Cofactors and Vitamins kegg subcategory 2.19e-02 4.68e-02 3/21
Global kegg category 3.00e-04 3.86e-03 11/21
Metabolism kegg subcategory 3.00e-04 3.86e-03 11/21
Metabolic pathways kegg pathway 2.18e-04 3.15e-03 11/21
Biosynthesis of secondary metabolites kegg pathway 1.40e-05 4.72e-04 8/21
Microbial metabolism in diverse environments kegg pathway 9.31e-03 2.64e-02 3/21

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 7.69e-04 1.29e-02 4/21
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 7.69e-04 1.52e-03 4/21

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 5.81e-03 1.03e-02 11/21
Amino acid transport and metabolism cog subcategory 2.67e-02 4.29e-02 3/21
Coenzyme transport and metabolism cog subcategory 1.77e-02 2.93e-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 104

There are 21 genes in Module 104

Gene Member Table (21)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0003 CDS 3774223 chromosome 2178 4511 + phosphoribosylformylglycinamidine synthase subunit II (EC 6.3.5.3) (IMGterm) False
Synpcc7942_0004 CDS 3774224 chromosome 4596 6077 + amidophosphoribosyltransferase (EC 2.4.2.14) (IMGterm) False
Synpcc7942_0051 CDS 3775764 chromosome 52606 54507 - TPR repeat False
Synpcc7942_0183 CDS 3775791 chromosome 181078 181467 + hypothetical protein False
Synpcc7942_0246 CDS 3773809 chromosome 242421 243500 + L-glutamate-binding protein / L-aspartate-binding protein / neutral amino acid-binding protein (IMGterm) False
Synpcc7942_0247 CDS 3773810 chromosome 243507 244640 + "amino acid ABC transporter membrane protein 1, PAAT family (TC 3.A.1.3.-) (IMGterm)" False
Synpcc7942_0314 CDS 3774835 chromosome 312403 313032 - succinate dehydrogenase subunit C (EC 1.3.5.1) (IMGterm) False
Synpcc7942_0414 CDS 3773359 chromosome 404016 405188 + hypothetical protein False
Synpcc7942_0583 CDS 3774821 chromosome 564123 565217 + protoporphyrin IX magnesium-chelatase (EC 6.6.1.1) (IMGterm) False
Synpcc7942_0640 CDS 3775623 chromosome 632225 633991 + ATPase False
Synpcc7942_0863 CDS 3774040 chromosome 866027 867208 + hypothetical protein False
Synpcc7942_1170 ispF CDS 3775476 chromosome 1203837 1204319 - MECDP-synthase (EC:4.6.1.12) False
Synpcc7942_1717 CDS 3775417 chromosome 1787724 1789025 - glycolate oxidase subunit (Fe-S) protein False
Synpcc7942_1718 CDS 3775418 chromosome 1789028 1790305 - glycolate oxidase subunit GlcE (EC:1.1.2.4) False
Synpcc7942_1898 CDS 3775261 chromosome 1970822 1972228 - "3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33) (IMGterm)" False
Synpcc7942_1964 ubiA CDS 3774149 chromosome 2034764 2035696 - 4-hydroxybenzoate octaprenyltransferase (EC 2.5.1.-) (IMGterm) False
Synpcc7942_2057 CDS 3774276 chromosome 2135125 2135757 + acyl-phosphate glycerol-3-phosphate acyltransferase (IMGterm) False
Synpcc7942_2084 CDS 3774303 chromosome 2164651 2165670 - chlorophyll synthase (EC 2.5.1.62) (IMGterm) False
Synpcc7942_2086 CDS 3774305 chromosome 2166791 2166991 - hypothetical protein False
Synpcc7942_2512 CDS 3774532 chromosome 2590765 2592123 - SSU ribosomal protein S12P methylthiotransferase (EC 2.-.-.-) (IMGterm) False
Synpcc7942_2513 CDS 3774533 chromosome 2592285 2593169 + Photosystem I assembly BtpA 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 104

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.