Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 43 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 43

There are 0 regulatory influences for Module 43

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
1649 3.90e+00 AGcCaATcgccgcAa
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1650 1.50e+00 tgcTGAAaccGctg.AGAa
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1651 3.30e+03 gttGCtgcAatgcctaAgcttttg
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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 43 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 8.60e-05 1.31e-03 6/29
Amino Acid Metabolism kegg subcategory 7.98e-03 3.79e-02 5/29
Transcription kegg subcategory 3.30e-05 6.31e-04 3/29
Metabolism kegg subcategory 9.45e-04 9.32e-03 17/29
Metabolism kegg category 1.26e-04 1.48e-03 20/29
Genetic Information Processing kegg category 8.61e-03 4.90e-02 6/29
Global kegg category 9.45e-04 8.32e-03 17/29
Metabolism kegg category 1.05e-02 2.81e-02 12/29
Oxidative phosphorylation kegg pathway 2.75e-03 1.40e-02 3/29
Nucleotide Metabolism kegg subcategory 1.15e-02 3.00e-02 3/29
Purine metabolism kegg pathway 3.77e-03 1.64e-02 3/29
Pyrimidine metabolism kegg pathway 1.06e-03 8.33e-03 3/29
Genetic Information Processing kegg category 3.51e-03 1.56e-02 6/29
Transcription kegg subcategory 3.30e-05 9.59e-04 3/29
RNA polymerase kegg pathway 3.30e-05 9.59e-04 3/29
Global kegg category 3.27e-03 1.52e-02 12/29
Metabolism kegg subcategory 3.27e-03 1.52e-02 12/29
Metabolic pathways kegg pathway 2.42e-03 1.32e-02 12/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Other tigr sub1role 2.50e-05 4.09e-04 3/29
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 2.02e-02 2.58e-02 3/29
Other tigr sub1role 2.50e-05 6.70e-05 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 2.22e-03 4.01e-02 4/29
Posttranslational modification, protein turnover, chaperones cog subcategory 3.56e-03 4.82e-02 4/29
Transcription cog subcategory 2.22e-03 4.11e-03 4/29
Posttranslational modification, protein turnover, chaperones cog subcategory 3.56e-03 6.43e-03 4/29
Energy production and conversion cog subcategory 1.78e-02 2.95e-02 4/29
Amino acid transport and metabolism cog subcategory 2.04e-02 3.35e-02 4/29
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 43

There are 29 genes in Module 43

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0165 CDS 3775773 chromosome 164986 165486 + hypothetical protein False
Synpcc7942_0166 CDS 3775774 chromosome 165483 166436 + asparaginase (EC 3.5.1.1) (IMGterm) False
Synpcc7942_0297 CDS 3773859 chromosome 294872 296713 + membrane protease FtsH catalytic subunit (EC 3.4.24.-) (IMGterm) False
Synpcc7942_0694 CDS 3775864 chromosome 687133 688056 - SSU ribosomal protein S1P (IMGterm) False
Synpcc7942_0942 CDS 3775329 chromosome 947957 949849 - membrane protease FtsH catalytic subunit (EC 3.4.24.-) (IMGterm) False
Synpcc7942_1085 CDS 3775035 chromosome 1099720 1102044 + glycogen branching enzyme (EC 2.4.1.18) (IMGterm) False
Synpcc7942_1178 CDS 3775484 chromosome 1210031 1211080 - photosystem II stability/assembly factor False
Synpcc7942_1179 CDS 3775485 chromosome 1211113 1211529 - rubredoxin 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_1184 CDS 3775490 chromosome 1214239 1215141 + 6-pyruvoyl-tetrahydropterin synthase-like protein (EC:4.2.3.12) False
Synpcc7942_1497 CDS 3773670 chromosome 1547545 1548105 - hypothetical protein False
Synpcc7942_1521 CDS 3774945 chromosome 1572849 1573646 + Sec-independent protein translocase TatD (EC 3.1.21.-) (IMGterm) 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_1524 CDS 3774948 chromosome 1579094 1583050 + DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) (IMGterm) True
Synpcc7942_1654 CDS 3775725 chromosome 1724849 1725232 - hypothetical protein False
Synpcc7942_1736 CDS 3775436 chromosome 1806290 1807075 + Iron-regulated ABC transporter ATPase subunit SufC (IMGterm) False
Synpcc7942_1737 CDS 3775437 chromosome 1807075 1808403 + Iron-regulated ABC transporter permease protein SufD (IMGterm) False
Synpcc7942_1738 CDS 3775438 chromosome 1808413 1809672 + cysteine desulfurase (EC 2.8.1.7) (IMGterm) False
Synpcc7942_1739 CDS 3775439 chromosome 1809717 1810142 + "transcriptional regulator, MerR family (IMGterm)" True
Synpcc7942_1846 CDS 3774421 chromosome 1911978 1913807 - hypothetical protein (EC:3.1.-) False
Synpcc7942_1847 CDS 3774422 chromosome 1913856 1914755 - dihydrodipicolinate synthase (EC 4.2.1.52) (IMGterm) False
Synpcc7942_1848 CDS 3774423 chromosome 1914772 1915836 - aspartate semialdehyde dehydrogenase (EC 1.2.1.11) (IMGterm) False
Synpcc7942_2299 rpsO CDS 3774582 chromosome 2369596 2369904 + SSU ribosomal protein S15P (IMGterm) False
Synpcc7942_2302 CDS 3774585 chromosome 2370891 2371247 - hypothetical protein False
Synpcc7942_2345 CDS 3774628 chromosome 2412588 2412926 - conserved hypothetical protein YCF65 False
Synpcc7942_2487 CDS 3774507 chromosome 2568613 2568831 + 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 43

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.