Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 5 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 5

There are 0 regulatory influences for Module 5

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
1535 1.30e+03 gGctgaTttgAcCA
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1536 6.70e+03 TtGgcTtTgCT
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1537 4.70e+04 t.AaTg.TgtCgacgTggtgG
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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 5 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 1.44e-03 1.25e-02 5/33
Translation kegg subcategory 0.00e+00 0.00e+00 10/33
Folding Sorting and Degradation kegg subcategory 1.56e-03 1.33e-02 3/33
Genetic Information Processing kegg category 0.00e+00 0.00e+00 14/33
Nucleotide Metabolism kegg subcategory 1.81e-02 4.09e-02 3/33
Purine metabolism kegg pathway 6.07e-03 2.04e-02 3/33
Genetic Information Processing kegg category 0.00e+00 0.00e+00 14/33
Translation kegg subcategory 0.00e+00 0.00e+00 10/33
Ribosome kegg pathway 0.00e+00 0.00e+00 9/33
Folding Sorting and Degradation kegg subcategory 1.56e-03 1.05e-02 3/33
RNA degradation kegg pathway 5.70e-05 1.38e-03 3/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 9/33
Other tigr sub1role 1.00e-06 3.00e-05 4/33
Protein synthesis tigr mainrole 0.00e+00 1.00e-05 10/33
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 6.34e-03 3.65e-02 4/33
Protein synthesis tigr mainrole 0.00e+00 0.00e+00 10/33
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 9/33
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 6.34e-03 9.73e-03 4/33
Other tigr sub1role 1.00e-06 3.00e-06 4/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 9.00e-06 11/33
Posttranslational modification, protein turnover, chaperones cog subcategory 1.40e-04 7.02e-03 6/33
Information storage and processing cog category 6.30e-05 3.18e-03 12/33
Information storage and processing cog category 4.50e-05 1.25e-04 12/33
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 0.00e+00 11/33
Posttranslational modification, protein turnover, chaperones cog subcategory 1.40e-04 3.31e-04 6/33
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 5

There are 33 genes in Module 5

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0098 CDS 3773438 chromosome 98302 100086 - pyruvate kinase (EC 2.7.1.40) (IMGterm) False
Synpcc7942_0260 CDS 3773822 chromosome 255961 258435 - ATPase False
Synpcc7942_0347 CDS 3774868 chromosome 340288 340452 + hypothetical protein False
Synpcc7942_0514 CDS 3774751 chromosome 499683 500105 - hypothetical protein False
Synpcc7942_0561 CDS 3774799 chromosome 542054 543049 + hypothetical protein False
Synpcc7942_0685 groEL CDS 3775855 chromosome 678881 680548 + Chaperonin Cpn60/TCP-1 False
Synpcc7942_1056 CDS 3773986 chromosome 1066706 1067488 + "transcriptional regulator, XRE family (IMGterm)" False
Synpcc7942_1059 CDS 3773989 chromosome 1068901 1069833 + hypothetical protein False
Synpcc7942_1443 CDS 3773615 chromosome 1497217 1498290 + fructose-bisphosphate aldolase (EC 4.1.2.13) (IMGterm) False
Synpcc7942_1524 CDS 3774948 chromosome 1579094 1583050 + DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) (IMGterm) True
Synpcc7942_1542 CDS 3774966 chromosome 1599353 1600381 - iron-stress chlorophyll-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_1735 CDS 3775435 chromosome 1804805 1806244 + Iron-regulated ABC transporter membrane component SufB (IMGterm) False
Synpcc7942_1736 CDS 3775436 chromosome 1806290 1807075 + Iron-regulated ABC transporter ATPase subunit SufC (IMGterm) False
Synpcc7942_1737 CDS 3775437 chromosome 1807075 1808403 + Iron-regulated ABC transporter permease protein SufD (IMGterm) False
Synpcc7942_1738 CDS 3775438 chromosome 1808413 1809672 + cysteine desulfurase (EC 2.8.1.7) (IMGterm) False
Synpcc7942_1926 CDS 3775289 chromosome 2001647 2001940 - hypothetical protein False
Synpcc7942_2215 rplO CDS 3773871 chromosome 2290963 2291406 - LSU ribosomal protein L15P (IMGterm) False
Synpcc7942_2217 rplR CDS 3773873 chromosome 2291990 2292352 - LSU ribosomal protein L18P (IMGterm) False
Synpcc7942_2218 rplF CDS 3773874 chromosome 2292352 2292891 - LSU ribosomal protein L6P (IMGterm) False
Synpcc7942_2221 rplX CDS 3773877 chromosome 2293939 2294280 - LSU ribosomal protein L24P (IMGterm) False
Synpcc7942_2222 rplN CDS 3773878 chromosome 2294280 2294645 - LSU ribosomal protein L14P (IMGterm) False
Synpcc7942_2223 rpsQ CDS 3773879 chromosome 2294657 2294905 - SSU ribosomal protein S17P (IMGterm) False
Synpcc7942_2225 rplP CDS 3773881 chromosome 2295137 2295565 - LSU ribosomal protein L16P (IMGterm) False
Synpcc7942_2226 rpsC CDS 3773882 chromosome 2295574 2296308 - SSU ribosomal protein S3P (IMGterm) False
Synpcc7942_2287 CDS 3774569 chromosome 2357146 2358120 - hypothetical protein False
Synpcc7942_2314 groES CDS 3774597 chromosome 2383296 2383607 - "GroES protein, 10 kD chaperonin" False
Synpcc7942_2338 CDS 3774621 chromosome 2405849 2406766 + hypothetical protein False
Synpcc7942_2437 ileS CDS 3774456 chromosome 2509504 2512368 - Isoleucyl-tRNA synthetase (EC 6.1.1.5) (IMGterm) False
Synpcc7942_2440 CDS 3774459 chromosome 2515544 2517694 - Polyribonucleotide nucleotidyltransferase (EC:2.7.7.8) False
Synpcc7942_2530 rpsB CDS 3775123 chromosome 2611383 2612138 + SSU ribosomal protein S2P (IMGterm) False
Synpcc7942_2533 CDS 3775126 chromosome 2613998 2614378 + hypothetical protein 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 5

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.