Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 107 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 107

There are 0 regulatory influences for Module 107

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
1841 8.10e-05 cgctCgatCtcccgCAGAcTc
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1842 3.40e+00 CAGTgTAgcGActgg
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1843 8.20e+02 CTgaGTtTTTcaAttcAagTt
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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 107 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein fate tigr mainrole 4.70e-05 2.09e-03 5/32
Protein fate tigr mainrole 4.70e-05 1.26e-04 5/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 1.14e-04 5.87e-03 6/32
Posttranslational modification, protein turnover, chaperones cog subcategory 1.14e-04 2.75e-04 6/32
Energy production and conversion cog subcategory 2.66e-02 4.27e-02 4/32
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 107

There are 32 genes in Module 107

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0073 CDS 3773790 chromosome 72000 73196 - hydroxymethylbutenyl pyrophosphate reductase (EC:1.17.1.2) False
Synpcc7942_0107 CDS 3773447 chromosome 106965 108383 - Small GTP-binding protein domain False
Synpcc7942_0176 CDS 3775784 chromosome 174311 174712 + hypothetical protein False
Synpcc7942_0240 CDS 3773803 chromosome 234851 235342 - hypothetical protein False
Synpcc7942_0301 CDS 3773863 chromosome 299628 299990 + single-strand binding protein (IMGterm) False
Synpcc7942_0364 CDS 3774885 chromosome 355865 356416 + hypothetical protein False
Synpcc7942_0450 CDS 3773395 chromosome 440050 440295 - putative NifU-like protein False
Synpcc7942_0487 CDS 3774725 chromosome 473510 474172 - signal peptidase I (EC 3.4.21.89). Serine peptidase. MEROPS family S26A (IMGterm) False
Synpcc7942_0559 hslO CDS 3774797 chromosome 540349 541242 - 33 kDa chaperonin False
Synpcc7942_0608 CDS 3775590 chromosome 595756 596298 + acireductone dioxygenase apoprotein (IMGterm) False
Synpcc7942_0638 CDS 3775621 chromosome 630050 630463 - Glyoxalase I (EC:4.4.1.5) False
Synpcc7942_0728 CDS 3775899 chromosome 723236 723781 + hypothetical protein False
Synpcc7942_0957 CDS 3775345 chromosome 965072 965719 + "cob(I)yrinic acid a,c-diamide adenosyltransferase (EC 2.5.1.17) (IMGterm)" False
Synpcc7942_0959 obgE CDS 3775347 chromosome 966530 967561 - GTP-binding protein False
Synpcc7942_0982 CDS 3775371 chromosome 991553 992167 + hypothetical protein False
Synpcc7942_0998 CDS 3773925 chromosome 1005621 1007519 + membrane protease FtsH catalytic subunit (EC 3.4.24.-) (IMGterm) False
Synpcc7942_1340 def CDS 3775533 chromosome 1374061 1374639 - peptide deformylase (EC 3.5.1.88) (IMGterm) False
Synpcc7942_1410 CDS 3774123 chromosome 1461949 1463571 - 2-isopropylmalate synthase (EC 2.3.3.13) (IMGterm) False
Synpcc7942_1554 CDS 3774978 chromosome 1611260 1611853 - ATP-dependent Clp protease proteolytic subunit ClpP (EC 3.4.21.92) (IMGterm) False
Synpcc7942_1627 CDS 3775696 chromosome 1695554 1696852 - hypothetical protein False
Synpcc7942_1698 CDS 3775397 chromosome 1765087 1765428 + putative transcriptional regulator True
Synpcc7942_1721 CDS 3775421 chromosome 1793212 1793916 - PBS lyase HEAT-like repeat False
Synpcc7942_1734 CDS 3775434 chromosome 1804395 1804757 + ferredoxin-thioredoxin reductase catalytic chain False
Synpcc7942_1746 CDS 3775446 chromosome 1816600 1817562 - group2 RNA polymerase sigma factor SigB True
Synpcc7942_1782 CDS 3774357 chromosome 1847829 1849121 - L-threonine synthase (EC 4.2.3.1) (IMGterm) False
Synpcc7942_1837 CDS 3774412 chromosome 1904030 1904374 - hypothetical protein False
Synpcc7942_2128 CDS 3773685 chromosome 2207506 2208081 - thioredoxin False
Synpcc7942_2129 CDS 3773686 chromosome 2208154 2208558 + iron-sulfur cluster binding protein False
Synpcc7942_2130 CDS 3773687 chromosome 2208566 2209150 + hypothetical protein False
Synpcc7942_2180 CDS 3773737 chromosome 2259490 2259927 - bacterioferritin comigratory protein (EC:1.11.1.15) False
Synpcc7942_2446 CDS 3774465 chromosome 2523086 2523919 - "methionine aminopeptidase, type I (EC 3.4.11.18) (IMGterm)" False
Synpcc7942_2447 CDS 3774466 chromosome 2524094 2524315 + 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 107

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.