Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 57 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 57

There are 0 regulatory influences for Module 57

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
1691 3.50e+03 ttagAa.CTTg
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1692 1.20e+04 aaTtatGgcTAAattCtGT
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1693 4.40e+04 tcAAcaaTttc.tTccaatAa
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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 57 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Small molecule interactions tigr sub1role 0.00e+00 3.00e-06 4/31
Other tigr sub1role 2.00e-06 5.70e-05 3/31
Regulatory functions tigr mainrole 3.00e-06 2.10e-04 4/31
Signal transduction tigr mainrole 2.00e-06 1.71e-04 3/31
sensory_box tigrfam 0.00e+00 0.00e+00 4/31
GGDEF tigrfam 2.00e-06 7.00e-06 3/31
Regulatory functions tigr mainrole 3.00e-06 9.00e-06 4/31
Small molecule interactions tigr sub1role 0.00e+00 0.00e+00 4/31
Signal transduction tigr mainrole 2.00e-06 7.00e-06 3/31
Other tigr sub1role 2.00e-06 7.00e-06 3/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 0.00e+00 0.00e+00 11/31
Cellular processes and signaling cog category 1.00e-06 1.08e-04 16/31
Cellular processes and signaling cog category 0.00e+00 1.00e-06 16/31
Signal transduction mechanisms cog subcategory 0.00e+00 0.00e+00 11/31
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain cog 1.00e-06 4.00e-06 3/31
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 57

There are 31 genes in Module 57

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0054 CDS 3775767 chromosome 56423 57190 - hypothetical protein False
Synpcc7942_0056 CDS 3775769 chromosome 57941 59068 - perosamine synthetase False
Synpcc7942_0081 CDS 3773798 chromosome 78987 79196 - RNA-binding S4 False
Synpcc7942_0151 CDS 3773491 chromosome 152527 154917 + response regulator receiver modulated diguanylate cyclase (IMGterm) False
Synpcc7942_0180 CDS 3775788 chromosome 177550 178422 - hypothetical protein False
Synpcc7942_0181 CDS 3775789 chromosome 178419 179792 - ATPase False
Synpcc7942_0366 CDS 3774887 chromosome 357549 359732 + putative sulfate transporter False
Synpcc7942_0406 CDS 3773351 chromosome 399953 400354 + hypothetical protein False
Synpcc7942_0490 CDS 3774728 chromosome 477395 479440 + diguanylate cyclase with PAS/PAC sensor (IMGterm) False
Synpcc7942_0562 CDS 3774800 chromosome 543141 543596 + hypothetical protein False
Synpcc7942_0729 CDS 3775900 chromosome 723806 724411 + hypothetical protein False
Synpcc7942_0759 CDS 3775932 chromosome 752574 753953 + hypothetical protein False
Synpcc7942_0761 CDS 3775934 chromosome 754779 755507 - hypothetical protein False
Synpcc7942_0870 CDS 3774047 chromosome 871886 872113 - hypothetical protein False
Synpcc7942_0871 CDS 3774048 chromosome 872106 872330 - hypothetical protein False
Synpcc7942_0983 CDS 3775372 chromosome 992187 992873 + deoxyribose-phosphate aldolase (EC:4.1.2.4) False
Synpcc7942_1158 CDS 3775108 chromosome 1189305 1192448 - diguanylate cyclase/phosphodiesterase with PAS/PAC and GAF sensor(s) (IMGterm) False
Synpcc7942_1208 CDS 3774445 chromosome 1234594 1234848 - Prevent-host-death protein False
Synpcc7942_1243 CDS 3773531 chromosome 1267422 1268117 - cyclic nucleotide-binding domain (cNMP-BD) protein False
Synpcc7942_1377 CDS 3775571 chromosome 1417540 1419879 + metal dependent phosphohydrolase (IMGterm) True
Synpcc7942_1382 CDS 3775576 chromosome 1427042 1429711 + diguanylate cyclase/phosphodiesterase (GGDEF & EAL domains) with PAS/PAC sensor(s) False
Synpcc7942_1384 CDS 3775578 chromosome 1430438 1431283 + hypothetical protein False
Synpcc7942_1643 CDS 3775713 chromosome 1710353 1711873 + diguanylate cyclase with GAF sensor (IMGterm) False
Synpcc7942_1716 CDS 3775415 chromosome 1783939 1787655 - diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s) (IMGterm) False
Synpcc7942_1803 CDS 3774378 chromosome 1873351 1873782 - "putative ferric uptake regulator, FUR family" True
Synpcc7942_1872 CDS 3775235 chromosome 1943951 1945399 + histidine kinase (EC 2.7.13.3) (IMGterm) False
Synpcc7942_1873 CDS 3775236 chromosome 1945396 1946076 + "two component transcriptional regulator, winged helix family (IMGterm)" True
Synpcc7942_2392 CDS 3774676 chromosome 2466045 2467505 + hypothetical protein False
Synpcc7942_2445 CDS 3774464 chromosome 2521920 2522933 - "phosphate ABC transporter substrate-binding protein, PhoT family (TC 3.A.1.7.1) (IMGterm)" False
Synpcc7942_2534 CDS 3775127 chromosome 2614395 2615660 - diguanylate cyclase with GAF sensor (IMGterm) False
Synpcc7942_2577 murQ CDS 3775173 chromosome 2662169 2663092 - Glucokinase regulatory-like protein (EC:4.2.-) 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 57

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.