Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 112 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 112

There are 0 regulatory influences for Module 112

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
1856 3.90e-03 TctcTTgcGgGgAcagctcga
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1857 6.50e-01 tCGGCTaTTgctatAcaGA
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1858 2.00e+02 AAtattGaCcaaGAgaTagGtAag
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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 112 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Energy Metabolism kegg subcategory 2.41e-04 3.16e-03 8/27
Metabolism kegg subcategory 5.60e-05 9.65e-04 18/27
Metabolism kegg category 1.10e-04 1.33e-03 19/27
Global kegg category 5.60e-05 7.05e-04 18/27
Metabolism kegg category 5.01e-03 1.88e-02 12/27
Energy Metabolism kegg subcategory 6.53e-04 6.37e-03 7/27
Photosynthesis kegg pathway 3.40e-05 9.59e-04 5/27
Global kegg category 1.55e-02 3.67e-02 10/27
Metabolism kegg subcategory 1.55e-02 3.67e-02 10/27
Metabolic pathways kegg pathway 1.22e-02 3.14e-02 10/27
Biosynthesis of secondary metabolites kegg pathway 4.12e-03 1.71e-02 6/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid biosynthesis tigr mainrole 1.10e-03 1.54e-02 3/27
Amino acid biosynthesis tigr mainrole 1.10e-03 2.09e-03 3/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 1.52e-02 2.54e-02 4/27
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 112

There are 27 genes in Module 112

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0114 CDS 3773454 chromosome 113327 113698 + hypothetical protein False
Synpcc7942_0224 psbN CDS 3775832 chromosome 223821 223961 - hypothetical protein False
Synpcc7942_0225 CDS 3775833 chromosome 224060 224263 + hypothetical protein False
Synpcc7942_0262 CDS 3773824 chromosome 259226 260620 + diaminopimelate decarboxylase (EC 4.1.1.20) (IMGterm) False
Synpcc7942_0323 CDS 3774844 chromosome 320046 320804 - Cytochrome c biogenesis protein-like False
Synpcc7942_0338 CDS 3774859 chromosome 333517 333834 + Ferredoxin (2Fe-2S) False
Synpcc7942_0343 CDS 3774864 chromosome 336654 337055 + photosystem II 11 kD protein False
Synpcc7942_0355 rbfA CDS 3774876 chromosome 348457 348870 - ribosome-binding factor A (IMGterm) False
Synpcc7942_0356 CDS 3774877 chromosome 348922 349146 - conserved hypothetical protein YCF33 False
Synpcc7942_0430 CDS 3773375 chromosome 419382 421292 + 1-deoxy-D-xylulose-5-phosphate synthase (EC 2.2.1.7) (IMGterm) False
Synpcc7942_0468 secG CDS 3773414 chromosome 454806 455045 - "preprotein translocase, SecG subunit" False
Synpcc7942_0679 CDS 3775662 chromosome 673785 674108 + RNA-binding region RNP-1 False
Synpcc7942_0890 CDS 3774068 chromosome 896748 901358 + glutamate synthase (ferredoxin) (EC 1.4.7.1) (IMGterm) False
Synpcc7942_1352 CDS 3775545 chromosome 1383192 1385162 + acetyl-coenzyme A synthetase (EC 6.2.1.1) (IMGterm) False
Synpcc7942_1505 CDS 3773678 chromosome 1554839 1555936 - 3-isopropylmalate dehydrogenase (EC 1.1.1.85) (IMGterm) False
Synpcc7942_1762 CDS 3775464 chromosome 1829577 1831028 + hypothetical protein False
Synpcc7942_1882 CDS 3775245 chromosome 1954814 1955224 - probable photosystem II 12 kD extrinsic protein False
Synpcc7942_1891 CDS 3775254 chromosome 1964412 1964972 + hypothetical protein False
Synpcc7942_2016 CDS 3774203 chromosome 2084803 2084922 - photosystem II PsbX protein False
Synpcc7942_2017 CDS 3774204 chromosome 2085077 2085370 + hypothetical protein False
Synpcc7942_2038 CDS 3774257 chromosome 2107367 2108059 - "transcriptional regulator, XRE family with cupin sensor domain" False
Synpcc7942_2188 CDS 3773745 chromosome 2266131 2267534 - isochorismate synthase (EC:5.4.4.2) False
Synpcc7942_2345 CDS 3774628 chromosome 2412588 2412926 - conserved hypothetical protein YCF65 False
Synpcc7942_2354 CDS 3774637 chromosome 2421202 2421726 - Peptidylprolyl isomerase (EC:5.2.1.8) False
Synpcc7942_2434 ilvH CDS 3774453 chromosome 2507663 2508181 + "acetolactate synthase, small subunit (EC 2.2.1.6) (IMGterm)" False
Synpcc7942_2481 CDS 3774501 chromosome 2561836 2563068 - hypothetical protein False
Synpcc7942_2483 CDS 3774503 chromosome 2563680 2565164 - 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 112

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.