Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 122 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 122

There are 0 regulatory influences for Module 122

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
1883 5.20e+00 tgccaatttCCcGaaAAacT
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1884 2.00e+02 tAAaAGttCTGaGctAGacaaGgC
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1885 9.90e+03 TcgcCaaGAccTGac
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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 122 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nucleotide Metabolism kegg subcategory 9.34e-03 4.22e-02 4/34
Nucleotide Metabolism kegg subcategory 2.00e-02 4.40e-02 3/34

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Unknown function tigr mainrole 6.77e-03 3.76e-02 3/34
Unknown function tigr mainrole 6.77e-03 1.03e-02 3/34

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 122

There are 34 genes in Module 122

Gene Member Table (34)
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_0044 CDS 3775757 chromosome 41495 43477 + hypothetical protein False
Synpcc7942_0050 CDS 3775763 chromosome 50070 52616 + hypothetical protein False
Synpcc7942_0153 CDS 3773493 chromosome 156026 156307 - hypothetical protein False
Synpcc7942_0164 CDS 3775772 chromosome 164548 164967 + Iojap-related protein False
Synpcc7942_0166 CDS 3775774 chromosome 165483 166436 + asparaginase (EC 3.5.1.1) (IMGterm) False
Synpcc7942_0356 CDS 3774877 chromosome 348922 349146 - conserved hypothetical protein YCF33 False
Synpcc7942_0419 CDS 3773364 chromosome 408941 409903 - biotin synthase (EC 2.8.1.6) (IMGterm) False
Synpcc7942_0464 CDS 3773410 chromosome 450539 450934 - hypothetical protein False
Synpcc7942_0477 CDS 3773423 chromosome 460994 461293 - conserved hypothetical protein YCF19 False
Synpcc7942_0667 CDS 3775650 chromosome 663985 664296 + hypothetical protein False
Synpcc7942_0669 CDS 3775652 chromosome 664540 665124 + DNA-3-methyladenine glycosylase (EC:3.2.2.21) False
Synpcc7942_0670 pyrB CDS 3775653 chromosome 665121 666137 + aspartate carbamoyltransferase (EC 2.1.3.2) (IMGterm) False
Synpcc7942_0787 CDS 3775964 chromosome 783007 783885 + putative purple acid phosphatase (EC:3.1.3.2) False
Synpcc7942_0916 CDS 3774094 chromosome 922848 922976 - 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_1006 CDS 3773934 chromosome 1017044 1018123 + TPR repeat False
Synpcc7942_1127 CDS 3775077 chromosome 1145373 1146842 + microcin-processing peptidase 2. Unknown type peptidase. MEROPS family U62 (IMGterm) False
Synpcc7942_1130 CDS 3775080 chromosome 1149445 1151259 + protein serine/threonine phosphatase (IMGterm) False
Synpcc7942_1221 CDS 3773509 chromosome 1242455 1242832 - response regulator receiver domain protein (CheY-like) False
Synpcc7942_1478 CDS 3773650 chromosome 1530415 1530852 - cytochrome CytM False
Synpcc7942_1519 hisD CDS 3774943 chromosome 1570976 1572280 - histidinol dehydrogenase (EC 1.1.1.23) (IMGterm) False
Synpcc7942_1600 CDS 3775666 chromosome 1666188 1667030 + "5',5'''-P-1,P-4-tetraphosphate phosphorylase II-like (EC:2.7.7.53)" False
Synpcc7942_1710 CDS 3775409 chromosome 1780048 1780278 + RNA polymerase subunit omega (rpoZ) (EC:2.7.7.6) False
Synpcc7942_1720 CDS 3775420 chromosome 1791952 1792392 + hypothetical protein False
Synpcc7942_1796 CDS 3774371 chromosome 1866456 1866749 - hypothetical protein False
Synpcc7942_1891 CDS 3775254 chromosome 1964412 1964972 + hypothetical protein False
Synpcc7942_2060 CDS 3774279 chromosome 2137504 2138169 - hypothetical protein False
Synpcc7942_2180 CDS 3773737 chromosome 2259490 2259927 - bacterioferritin comigratory protein (EC:1.11.1.15) False
Synpcc7942_2320 CDS 3774603 chromosome 2389796 2390083 + hypothetical protein False
Synpcc7942_2436 CDS 3774455 chromosome 2508849 2509445 - peptide methionine sulfoxide reductase (EC:1.8.4.11) False
Synpcc7942_2561 CDS 3775154 chromosome 2639146 2639982 - Delta-9 acyl-phospholipid desaturase (EC 1.14.19.-) (IMGterm) False
Synpcc7942_2578 CDS 3775174 chromosome 2663093 2663566 - hypothetical protein False
Synpcc7942_2580 CDS 3775176 chromosome 2664460 2666709 - Heat shock protein Hsp70 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 122

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.