Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 181 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 181

There are 0 regulatory influences for Module 181

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
2060 5.90e+00 tccCGAtCgcttgg
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2061 3.70e+02 taGtcTAaGcttAAaTtCTa
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2062 6.70e+03 tTTGgtgCTG
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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 181 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Replication and Repair kegg subcategory 9.65e-03 4.27e-02 3/28
Genetic Information Processing kegg category 3.03e-04 3.19e-03 8/28
Energy Metabolism kegg subcategory 1.73e-02 3.95e-02 5/28
Oxidative phosphorylation kegg pathway 2.41e-03 1.32e-02 3/28
Genetic Information Processing kegg category 2.83e-03 1.42e-02 6/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 3.28e-02 3.96e-02 3/28

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 181

There are 28 genes in Module 181

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0012 rpsF CDS 3774232 chromosome 11641 11964 - SSU ribosomal protein S6P (IMGterm) False
Synpcc7942_0079 CDS 3773796 chromosome 77138 77584 - conserved hypothetical protein YCF41 False
Synpcc7942_0139 CDS 3773479 chromosome 140268 142106 + "acetolactate synthase, large subunit (EC 2.2.1.6) (IMGterm)" False
Synpcc7942_0164 CDS 3775772 chromosome 164548 164967 + Iojap-related protein False
Synpcc7942_0289 secA CDS 3773851 chromosome 284148 286994 + protein translocase subunit secA (IMGterm) False
Synpcc7942_0301 CDS 3773863 chromosome 299628 299990 + single-strand binding protein (IMGterm) False
Synpcc7942_0343 CDS 3774864 chromosome 336654 337055 + photosystem II 11 kD protein False
Synpcc7942_0410 CDS 3773355 chromosome 401750 402022 - hypothetical protein 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_0514 CDS 3774751 chromosome 499683 500105 - hypothetical protein False
Synpcc7942_0549 CDS 3774787 chromosome 531884 532645 + hypothetical protein False
Synpcc7942_0728 CDS 3775899 chromosome 723236 723781 + hypothetical protein False
Synpcc7942_0956 CDS 3775344 chromosome 963926 965068 + hypothetical protein False
Synpcc7942_1016 CDS 3773944 chromosome 1030953 1031435 - CheW protein (IMGterm) False
Synpcc7942_1127 CDS 3775077 chromosome 1145373 1146842 + microcin-processing peptidase 2. Unknown type peptidase. MEROPS family U62 (IMGterm) False
Synpcc7942_1180 CDS 3775486 chromosome 1211703 1212104 + NADH dehydrogenase subunit A (EC 1.6.5.3) (IMGterm) False
Synpcc7942_1181 CDS 3775487 chromosome 1212095 1212802 + NADH dehydrogenase subunit B (EC 1.6.5.3) (IMGterm) False
Synpcc7942_1182 CDS 3775488 chromosome 1212795 1213313 + NADH dehydrogenase subunit C (EC 1.6.5.3) (IMGterm) False
Synpcc7942_1710 CDS 3775409 chromosome 1780048 1780278 + RNA polymerase subunit omega (rpoZ) (EC:2.7.7.6) False
Synpcc7942_1750 CDS 3775450 chromosome 1820146 1820532 - conserved hypothetical protein YCF35 False
Synpcc7942_1751 CDS 3775451 chromosome 1820575 1820778 - hypothetical protein False
Synpcc7942_1860 CDS 3775223 chromosome 1930475 1931182 - "two component transcriptional regulator, LuxR family (IMGterm)" True
Synpcc7942_1882 CDS 3775245 chromosome 1954814 1955224 - probable photosystem II 12 kD extrinsic protein False
Synpcc7942_2046 CDS 3774265 chromosome 2118062 2118451 + glycine cleavage system H protein False
Synpcc7942_2264 CDS 3774546 chromosome 2332654 2332929 - "transcriptional regulator, LuxR family (IMGterm)" True
Synpcc7942_2321 CDS 3774604 chromosome 2390121 2390642 + TPR repeat False
Synpcc7942_2322 CDS 3774605 chromosome 2390654 2390944 + aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C (EC 6.3.5.-) (IMGterm) 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 181

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.