Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 19 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 19

There are 0 regulatory influences for Module 19

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
1577 1.40e+00 gggaCGATCGC
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1578 1.90e+03 cCTtaa.tgtatTGAtatgaagaT
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1579 8.60e+02 CTgAGtcagcatttc
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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 19 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 1.02e-03 9.92e-03 5/31
Nucleotide Metabolism kegg subcategory 1.46e-02 3.51e-02 3/31
Purine metabolism kegg pathway 4.83e-03 1.83e-02 3/31

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 4.81e-03 3.32e-02 4/31
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 4.81e-03 7.65e-03 4/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 6.25e-03 1.11e-02 4/31
Function unknown cog subcategory 2.84e-02 4.54e-02 4/31
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 19

There are 31 genes in Module 19

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0110 CDS 3773450 chromosome 109390 109947 + "transcriptional regulator, XRE family (IMGterm)" False
Synpcc7942_0129 CDS 3773469 chromosome 128446 128877 + "Resolvase, RNase H-like fold" False
Synpcc7942_0180 CDS 3775788 chromosome 177550 178422 - hypothetical protein False
Synpcc7942_0181 CDS 3775789 chromosome 178419 179792 - ATPase False
Synpcc7942_0292 CDS 3773854 chromosome 288534 289760 + Phosphopantothenate-cysteine ligase (EC 6.3.2.5) / Phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) (IMGterm) False
Synpcc7942_0302 CDS 3773864 chromosome 300008 301447 - Phospholipase D/Transphosphatidylase False
Synpcc7942_0306 CDS 3773868 chromosome 304039 304347 - hypothetical protein False
Synpcc7942_0784 CDS 3775961 chromosome 779531 779848 + hypothetical protein False
Synpcc7942_0947 CDS 3775335 chromosome 955647 956714 - "carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-) (IMGterm)" False
Synpcc7942_0948 CDS 3775336 chromosome 956719 957546 - "carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-) (IMGterm)" False
Synpcc7942_0949 CDS 3775337 chromosome 957546 958424 - "carbohydrate ABC transporter membrane protein 1, CUT1 family (TC 3.A.1.1.-) (IMGterm)" False
Synpcc7942_0979 CDS 3775367 chromosome 988074 988577 - hypothetical protein False
Synpcc7942_1032 CDS 3773962 chromosome 1046506 1047972 + hypothetical protein False
Synpcc7942_1033 CDS 3773963 chromosome 1047992 1048948 + hypothetical protein False
Synpcc7942_1160 CDS 3775110 chromosome 1193397 1194299 + hypothetical protein False
Synpcc7942_1166 CDS 3775471 chromosome 1199437 1200762 + hypothetical protein False
Synpcc7942_1337 CDS 3775530 chromosome 1368411 1372715 + Integrins alpha chain False
Synpcc7942_1419 chlL CDS 3773591 chromosome 1472585 1473445 + "light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein (EC:1.18.-)" False
Synpcc7942_1420 CDS 3773592 chromosome 1473509 1474909 + "light-independent protochlorophyllide reductase, N subunit (EC:1.18.-)" False
Synpcc7942_1467 CDS 3773639 chromosome 1520674 1521363 + Heat shock protein DnaJ-like False
Synpcc7942_1522 rpoB CDS 3774946 chromosome 1573729 1577031 + DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) (IMGterm) True
Synpcc7942_1523 CDS 3774947 chromosome 1577150 1579024 + DNA-directed RNA polymerase gamma chain (EC 2.7.7.6) (IMGterm) True
Synpcc7942_1544 CDS 3774968 chromosome 1600802 1601053 + panthotenate metabolism flavoprotein False
Synpcc7942_1677 CDS 3775749 chromosome 1745500 1746597 - hypothetical protein False
Synpcc7942_1748 CDS 3775448 chromosome 1818990 1819751 - hypothetical protein False
Synpcc7942_1824 CDS 3774399 chromosome 1895166 1895630 - CBS False
Synpcc7942_2079 CDS 3774298 chromosome 2156574 2157755 - acetate kinase (EC 2.7.2.1) (IMGterm) False
Synpcc7942_2150 CDS 3773707 chromosome 2232979 2234022 + penicillin amidase (EC 3.5.1.11). Cysteine peptidase. MEROPS family C59 (IMGterm) False
Synpcc7942_2195 CDS 3773752 chromosome 2272975 2274900 - putative adenylate/guanylate cyclase (EC:4.6.1.1) False
Synpcc7942_2253 CDS 3773909 chromosome 2322145 2323299 - "Glutamate--cysteine ligase, putative" False
Synpcc7942_2279 CDS 3774561 chromosome 2347614 2349026 + ammonium transporter (TC 1.A.11) (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 19

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.