Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 105 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 105

There are 0 regulatory influences for Module 105

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
1835 1.10e+01 AaTCcTaAGaaattgTaAAatT
Loader icon
1836 6.10e+01 cGaTaaCAGCgAc
Loader icon
1837 6.00e+03 tTttcTt..g.ctT.gtTTag
Loader icon
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 105 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 6.30e-04 6.91e-03 6/21
Signal Transduction kegg subcategory 0.00e+00 1.50e-05 5/21
Metabolism kegg subcategory 1.31e-03 1.17e-02 13/21
Metabolism kegg category 1.57e-03 1.17e-02 14/21
Environmental Information Processing kegg category 1.94e-04 2.18e-03 5/21
Global kegg category 1.31e-03 1.02e-02 13/21
Environmental Information Processing kegg category 1.72e-04 2.71e-03 5/21
Signal Transduction kegg subcategory 0.00e+00 2.40e-05 5/21
Two-component system kegg pathway 0.00e+00 2.40e-05 5/21
Biosynthesis of secondary metabolites kegg pathway 4.67e-03 1.82e-02 5/21

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 1.30e-05 1.40e-03 6/21
Cell motility cog subcategory 3.70e-05 2.65e-03 3/21
Cellular processes and signaling cog category 9.11e-04 2.45e-02 9/21
Signal transduction mechanisms cog subcategory 1.30e-05 3.80e-05 6/21
Cell motility cog subcategory 3.70e-05 1.02e-04 3/21
General function prediction only cog subcategory 1.06e-02 1.82e-02 5/21
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 105

There are 21 genes in Module 105

Gene Member Table (21)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0156 CDS 3773496 chromosome 157210 158841 - phosphoglucomutase (EC:5.4.2.2) False
Synpcc7942_0214 CDS 3775822 chromosome 216509 217432 + hypothetical protein False
Synpcc7942_0375 CDS 3774896 chromosome 368929 370344 - processing protease False
Synpcc7942_0376 CDS 3774897 chromosome 370341 371867 - putative zinc protease protein False
Synpcc7942_0377 CDS 3774898 chromosome 371868 372206 - hypothetical protein False
Synpcc7942_0411 trpA CDS 3773356 chromosome 402191 402991 - "tryptophan synthase, alpha chain (EC 4.2.1.20) (IMGterm)" False
Synpcc7942_0415 CDS 3773360 chromosome 405168 406145 - hypothetical protein False
Synpcc7942_0469 CDS 3773415 chromosome 455066 456664 - phosphoglycerate mutase (EC 5.4.2.1) (IMGterm) False
Synpcc7942_0645 CDS 3775628 chromosome 639397 640758 + "glutamate-1-semialdehyde 2,1-aminomutase (EC 5.4.3.8) (IMGterm)" False
Synpcc7942_0657 CDS 3775640 chromosome 653047 653388 - hypothetical protein False
Synpcc7942_0674 CDS 3775657 chromosome 669347 670300 + coproporphyrinogen oxidase (EC 1.3.3.3) (IMGterm) False
Synpcc7942_0855 CDS 3774032 chromosome 853629 854882 + response regulator receiver domain protein (CheY-like) False
Synpcc7942_0856 CDS 3774033 chromosome 854933 855295 + response regulator receiver domain protein (CheY-like) False
Synpcc7942_0857 CDS 3774034 chromosome 855315 855821 + CheW protein (IMGterm) False
Synpcc7942_0858 CDS 3774035 chromosome 855893 860113 + methyl-accepting chemotaxis sensory transducer with phytochrome sensor (IMGterm) False
Synpcc7942_0859 CDS 3774036 chromosome 860118 862976 + CheA signal transduction histidine kinase (IMGterm) False
Synpcc7942_0930 fabZ CDS 3774929 chromosome 937912 938379 + 3-hydroxyacyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.-) (IMGterm) False
Synpcc7942_0941 CDS 3775328 chromosome 946064 947773 - ATPase False
Synpcc7942_1080 CDS 3775029 chromosome 1091781 1093124 + K+ transporter Trk False
Synpcc7942_1254 CDS 3773542 chromosome 1277460 1277855 + cyclic nucleotide-binding domain (cNMP-BD) protein False
Synpcc7942_1341 CDS 3775534 chromosome 1374756 1375841 + 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 105

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.