Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 73 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 73

There are 0 regulatory influences for Module 73

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
1739 2.90e+01 AgaaGTttgaTgTtaatggTTACA
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1740 1.20e+03 ttaGcgaTgTTGAGt.gTgtc
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1741 8.30e+03 TcatgAccccTcTtGTCAtcC
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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 73 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 5.53e-03 9.86e-03 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 73

There are 32 genes in Module 73

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0042 rpmB CDS 3775755 chromosome 40855 41091 - LSU ribosomal protein L28P (IMGterm) False
Synpcc7942_0052 CDS 3775765 chromosome 54512 55030 - hypothetical protein False
Synpcc7942_0221 glk CDS 3775829 chromosome 221498 222535 + glucokinase (EC 2.7.1.2) (IMGterm) False
Synpcc7942_0240 CDS 3773803 chromosome 234851 235342 - hypothetical protein False
Synpcc7942_0241 CDS 3773804 chromosome 235487 236854 + 23S rRNA m(5)U-1939 methyltransferase (EC 2.1.1.-) (IMGterm) False
Synpcc7942_0425 CDS 3773370 chromosome 415064 415441 - hypothetical protein False
Synpcc7942_0465 CDS 3773411 chromosome 451023 451748 - hypothetical protein False
Synpcc7942_0548 CDS 3774786 chromosome 530623 531783 - hypothetical protein False
Synpcc7942_0623 CDS 3775606 chromosome 613972 615351 + thioredoxin reductase (EC:1.8.1.9) False
Synpcc7942_0624 CDS 3775607 chromosome 615361 616419 + light dependent period False
Synpcc7942_0625 CDS 3775608 chromosome 616419 618185 + Single-stranded nucleic acid binding R3H False
Synpcc7942_0658 CDS 3775641 chromosome 653558 653770 - hypothetical protein False
Synpcc7942_0771 CDS 3775948 chromosome 763640 764854 - hypothetical protein (EC:2.5.1.18) False
Synpcc7942_0801 CDS 3775978 chromosome 795123 795812 + Superoxide dismutase (EC:1.15.1.1) False
Synpcc7942_0843 CDS 3774020 chromosome 838504 838935 - hypothetical protein False
Synpcc7942_0880 CDS 3774057 chromosome 886915 887472 - hypothetical protein False
Synpcc7942_1167 CDS 3775473 chromosome 1200773 1201330 - hypothetical protein False
Synpcc7942_1297 CDS 3773586 chromosome 1322910 1324319 + Malate dehydrogenase (oxaloacetate decarboxylating) (EC:1.1.1.38) False
Synpcc7942_1302 CDS 3775938 chromosome 1330250 1330726 + hypothetical protein False
Synpcc7942_1409 CDS 3774122 chromosome 1460847 1461869 + iron transport system substrate-binding protein False
Synpcc7942_1673 CDS 3775745 chromosome 1743189 1743854 - hypothetical protein False
Synpcc7942_1862 CDS 3775225 chromosome 1932765 1933688 + hypothetical protein False
Synpcc7942_1866 CDS 3775229 chromosome 1936389 1936799 - hypothetical protein False
Synpcc7942_1942 CDS 3775305 chromosome 2015645 2016097 + bacterioferritin comigratory protein-like (EC:1.11.1.15) False
Synpcc7942_1952 CDS 3774137 chromosome 2025399 2025740 + hypothetical protein False
Synpcc7942_2038 CDS 3774257 chromosome 2107367 2108059 - "transcriptional regulator, XRE family with cupin sensor domain" False
Synpcc7942_2281 CDS 3774563 chromosome 2350198 2351154 + hypothetical protein False
Synpcc7942_2309 CDS 3774592 chromosome 2377107 2377703 - thioredoxin peroxidase (EC:1.11.1.15) False
Synpcc7942_2402 CDS 3774686 chromosome 2476025 2477155 + agmatine deiminase (EC 3.5.3.12) (IMGterm) False
Synpcc7942_2466 CDS 3774486 chromosome 2546850 2547557 + "two component transcriptional regulator, winged helix family (IMGterm)" True
Synpcc7942_2575 CDS 3775168 chromosome 2654163 2655104 + Mn transporter MntC False
Synpcc7942_2608 CDS 3775205 chromosome 2691104 2691424 + 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 73

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.