Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 179 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 179

There are 0 regulatory influences for Module 179

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
2054 2.90e-03 TtGtcagTccTC.agAgtTt
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2055 3.40e+00 CAAAAAttcTGaATtctctg
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2056 3.50e+02 agaGCcattCAg..CatgacG
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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 179 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Cofactors and Vitamins kegg subcategory 1.15e-02 4.70e-02 5/37
Metabolism of Cofactors and Vitamins kegg subcategory 1.15e-02 2.99e-02 5/37
One carbon pool by folate kegg pathway 2.30e-05 7.30e-04 3/37

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 2.66e-03 4.37e-02 5/37
Carbohydrate transport and metabolism cog subcategory 2.66e-03 4.88e-03 5/37
Nucleotide transport and metabolism cog subcategory 1.13e-02 1.93e-02 3/37
General function prediction only cog subcategory 1.90e-02 3.14e-02 7/37
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 179

There are 37 genes in Module 179

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0135 CDS 3773475 chromosome 136016 136651 - Methylase involved in ubiquinone/menaquinone biosynthesis-like (EC:2.1.1.-) False
Synpcc7942_0154 CDS 3773494 chromosome 156340 156957 + hypothetical protein False
Synpcc7942_0339 CDS 3774860 chromosome 333995 335074 + hypothetical protein False
Synpcc7942_0340 CDS 3774861 chromosome 335071 335652 + hypothetical protein False
Synpcc7942_0373 CDS 3774894 chromosome 366738 368024 - hypothetical protein False
Synpcc7942_0498 CDS 3774736 chromosome 484585 487098 + "mannose-1-phosphate guanyltransferase (EC:5.4.2.8, EC:2.7.7.13)" False
Synpcc7942_0566 CDS 3774804 chromosome 547262 548017 + HAD-superfamily hydrolase subfamily IIB False
Synpcc7942_0568 CDS 3774806 chromosome 549371 550687 - cytosine deaminase (EC:3.5.4.1) False
Synpcc7942_0671 CDS 3775654 chromosome 666156 666653 + hypothetical protein False
Synpcc7942_0692 CDS 3775862 chromosome 685631 686185 - hypothetical protein False
Synpcc7942_0756 CDS 3775929 chromosome 750406 750870 + "chain A, D20c mutant of T4 lysozyme (EC:3.2.1.17)" False
Synpcc7942_0763 CDS 3775939 chromosome 756989 757318 - "transcriptional regulator, XRE family (IMGterm)" True
Synpcc7942_0784 CDS 3775961 chromosome 779531 779848 + hypothetical protein False
Synpcc7942_0791 CDS 3775968 chromosome 785973 787211 - polyA polymerase (EC:2.7.7.19) False
Synpcc7942_0958 purN CDS 3775346 chromosome 965726 966355 - formyltetrahydrofolate-dependent phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (IMGterm) False
Synpcc7942_1019 CDS 3773947 chromosome 1033300 1034799 + 4-alpha-glucanotransferase (IMGterm) False
Synpcc7942_1020 CDS 3773948 chromosome 1034796 1035746 + O-succinylbenzoate-CoA synthase-like (EC:4.2.1.113) False
Synpcc7942_1044 CDS 3773974 chromosome 1056740 1057462 - thymidylate synthase (FAD) (EC 2.1.1.148) (IMGterm) False
Synpcc7942_1155 CDS 3775105 chromosome 1182479 1183195 + hypothetical protein False
Synpcc7942_1218 CDS 3773506 chromosome 1240557 1241411 - circadian clock protein KaiA False
Synpcc7942_1222 truB CDS 3773510 chromosome 1242925 1243809 + tRNA pseudouridine synthase B (EC 4.2.1.70) (IMGterm) False
Synpcc7942_1242 CDS 3773530 chromosome 1266128 1267057 + "transcriptional regulator, LysR family (IMGterm)" True
Synpcc7942_1260 CDS 3773549 chromosome 1283244 1284071 + hypothetical protein False
Synpcc7942_1301 CDS 3775937 chromosome 1328678 1330141 + ATP-dependent DNA helicase RecQ (EC 3.6.1.-) (IMGterm) False
Synpcc7942_1371 CDS 3775565 chromosome 1408205 1409368 - magnesium and cobalt transport protein CorA False
Synpcc7942_1372 CDS 3775566 chromosome 1409560 1413132 + methionine synthase (B12-dependent) (EC 2.1.1.13) (IMGterm) False
Synpcc7942_1696 CDS 3775395 chromosome 1763712 1764452 - hypothetical protein False
Synpcc7942_1725 CDS 3775425 chromosome 1797616 1799067 + "transcriptional regulator, GntR family (IMGterm)" True
Synpcc7942_1767 CDS 3775469 chromosome 1834078 1835490 - cytochrome bd plastoquinol oxidase subunit 1 apoprotein (EC 1.10.3.-) (IMGterm) False
Synpcc7942_1769 CDS 3774344 chromosome 1836408 1836794 + hypothetical protein False
Synpcc7942_1918 CDS 3775281 chromosome 1993521 1994600 + UDP-glucose:tetrahydrobiopterin glucosyltransferase (EC:2.4.1.-) False
Synpcc7942_1985 CDS 3774172 chromosome 2055445 2056338 - hypothetical protein False
Synpcc7942_2278 CDS 3774560 chromosome 2345093 2347240 + hypothetical protein False
Synpcc7942_2394 CDS 3774678 chromosome 2469054 2470835 - "sodium/proton antiporter, CPA1 family (TC 2.A.36) (IMGterm)" False
Synpcc7942_2404 CDS 3774688 chromosome 2477807 2478547 + hypothetical protein False
Synpcc7942_2462 CDS 3774482 chromosome 2542826 2544106 - probable sugar kinase (EC:2.7.1.17) False
Synpcc7942_2464 CDS 3774484 chromosome 2545468 2546166 - N-acylglucosamine-6-phosphate 2-epimerase (EC:5.1.3.9) 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 179

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.