Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 29 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 29

There are 0 regulatory influences for Module 29

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
1607 1.00e+00 gaTgGGtgGcGaAgcGGCacTCa
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1608 2.20e+00 CtcTAcaCTGaAgAA
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1609 5.50e+01 aaTTgA.AAt.AA.ttca.AagAt
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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 29 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Membrane Transport kegg subcategory 1.11e-02 4.64e-02 3/32
Membrane Transport kegg subcategory 1.11e-02 2.92e-02 3/32
ABC transporters kegg pathway 6.27e-03 2.09e-02 3/32

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Other tigr sub1role 3.70e-05 5.54e-04 3/32
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 1.14e-04 3.75e-03 6/32
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 1.14e-04 2.75e-04 6/32
Other tigr sub1role 3.70e-05 9.90e-05 3/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 8.75e-04 2.14e-02 5/32
Cellular processes and signaling cog category 1.82e-02 3.02e-02 9/32
Posttranslational modification, protein turnover, chaperones cog subcategory 8.75e-04 1.70e-03 5/32
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 29

There are 32 genes in Module 29

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_0322 CDS 3774843 chromosome 318679 320049 - c-type cytochrome biogenesis protein False
Synpcc7942_0323 CDS 3774844 chromosome 320046 320804 - Cytochrome c biogenesis protein-like False
Synpcc7942_0355 rbfA CDS 3774876 chromosome 348457 348870 - ribosome-binding factor A (IMGterm) False
Synpcc7942_0395 CDS 3774916 chromosome 388494 389618 + hypothetical protein False
Synpcc7942_0622 CDS 3775604 chromosome 611915 613912 + ATPase False
Synpcc7942_0803 CDS 3775981 chromosome 796507 797289 - hypothetical protein False
Synpcc7942_0851 CDS 3774028 chromosome 847233 848258 + phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (IMGterm) False
Synpcc7942_0887 rpsL CDS 3774064 chromosome 893750 894124 - SSU ribosomal protein S12P (IMGterm) False
Synpcc7942_0909 CDS 3774087 chromosome 918135 918491 + HesB/YadR/YfhF False
Synpcc7942_1096 CDS 3775046 chromosome 1113354 1114724 - hydroxymethylpyrimidine synthase (IMGterm) False
Synpcc7942_1124 CDS 3775074 chromosome 1141288 1143300 + Exoribonuclease II (EC:3.1.13.1) False
Synpcc7942_1256 CDS 3773544 chromosome 1279079 1279633 + glutathione S-transferase (EC:2.5.1.18) False
Synpcc7942_1259 CDS 3773548 chromosome 1281993 1283171 + arsenite efflux ATP-binding protein ArsA (TC 3.A.4.1.1) (IMGterm) False
Synpcc7942_1358 CDS 3775551 chromosome 1397087 1397878 - hypothetical protein False
Synpcc7942_1362 CDS 3775556 chromosome 1401672 1402157 + hypothetical protein False
Synpcc7942_1398 CDS 3774111 chromosome 1447847 1450069 - Cellulose synthase (UDP-forming) (EC:2.4.1.12) False
Synpcc7942_1399 CDS 3774112 chromosome 1450087 1451241 - hypothetical protein False
Synpcc7942_1406 CDS 3774119 chromosome 1456803 1457909 - ATPase (EC:3.6.3.30) False
Synpcc7942_1407 CDS 3774120 chromosome 1458057 1459688 + iron(III) ABC transporter permease protein False
Synpcc7942_1754 CDS 3775455 chromosome 1822345 1822497 - hypothetical protein False
Synpcc7942_1787 CDS 3774362 chromosome 1854247 1854729 - SUF system FeS assembly protein False
Synpcc7942_1907 CDS 3775270 chromosome 1983417 1984493 - Mg-protoporphyrin IX monomethyl ester (oxidative) cyclase (EC 1.14.13.81) (IMGterm) False
Synpcc7942_1930 CDS 3775293 chromosome 2004305 2005048 + hypothetical protein False
Synpcc7942_1989 CDS 3774176 chromosome 2059907 2060818 - cation diffusion facilitator family transporter False
Synpcc7942_2113 CDS 3774332 chromosome 2193730 2194725 + ribose-phosphate pyrophosphokinase (EC:2.7.6.1) False
Synpcc7942_2137 CDS 3773694 chromosome 2216508 2220563 + cobaltochelatase CobN subunit (EC 6.6.1.2) (IMGterm) False
Synpcc7942_2190 CDS 3773747 chromosome 2267935 2268357 + Methionine sulfoxide reductase B (EC:1.8.4.12) False
Synpcc7942_2383 CDS 3774667 chromosome 2450109 2451260 + "Nucleotide binding protein, PINc" False
Synpcc7942_2519 CDS 3774539 chromosome 2599191 2601896 - diguanylate cyclase/phosphodiesterase (IMGterm) False
Synpcc7942_2537 clpP CDS 3775130 chromosome 2619632 2620231 - ATP-dependent Clp protease proteolytic subunit ClpP (EC 3.4.21.92) (IMGterm) False
Synpcc7942_2605 CDS 3775202 chromosome 2687378 2688034 - 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 29

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.