Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 198 Profile

GeneModule member RegulatorRegulator MotifMotif
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 198

There are 0 regulatory influences for Module 198

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
2111 2.50e-01 C.gcc.gatCGaTagaCTgg
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2112 4.30e+03 CtGtTtctcacCaAACcgcTcC
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2113 8.50e+03 CcgCcTAgaATGAA
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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 198 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Biosynthesis of secondary metabolites kegg pathway 1.42e-02 3.46e-02 5/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein fate tigr mainrole 1.00e-06 6.90e-05 6/26
Amino acid biosynthesis tigr mainrole 9.52e-04 1.44e-02 3/26
Protein fate tigr mainrole 1.00e-06 2.00e-06 6/26
Amino acid biosynthesis tigr mainrole 9.52e-04 1.83e-03 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Intracellular trafficking, secretion, and vesicular transport cog subcategory 2.00e-06 1.99e-04 5/26
Posttranslational modification, protein turnover, chaperones cog subcategory 2.70e-05 2.09e-03 6/26
Cellular processes and signaling cog category 8.10e-05 3.80e-03 12/26
Cellular processes and signaling cog category 3.55e-03 6.42e-03 9/26
Intracellular trafficking, secretion, and vesicular transport cog subcategory 2.00e-06 4.00e-06 5/26
Posttranslational modification, protein turnover, chaperones cog subcategory 2.70e-05 7.50e-05 6/26
Amino acid transport and metabolism cog subcategory 1.29e-02 2.19e-02 4/26
Protease subunit of ATP-dependent Clp proteases cog 0.00e+00 0.00e+00 3/26
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 198

There are 26 genes in Module 198

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0080 CDS 3773797 chromosome 77648 78871 - probable ABC transporter permease protein False
Synpcc7942_0289 secA CDS 3773851 chromosome 284148 286994 + protein translocase subunit secA (IMGterm) False
Synpcc7942_0450 CDS 3773395 chromosome 440050 440295 - putative NifU-like protein False
Synpcc7942_0473 CDS 3773419 chromosome 459096 460202 + NADH:flavin oxidoreductase Old Yellow Enzyme family-like (EC:1.-) False
Synpcc7942_0487 CDS 3774725 chromosome 473510 474172 - signal peptidase I (EC 3.4.21.89). Serine peptidase. MEROPS family S26A (IMGterm) False
Synpcc7942_0549 CDS 3774787 chromosome 531884 532645 + hypothetical protein False
Synpcc7942_0622 CDS 3775604 chromosome 611915 613912 + ATPase False
Synpcc7942_0638 CDS 3775621 chromosome 630050 630463 - Glyoxalase I (EC:4.4.1.5) False
Synpcc7942_0956 CDS 3775344 chromosome 963926 965068 + hypothetical protein False
Synpcc7942_0959 obgE CDS 3775347 chromosome 966530 967561 - GTP-binding protein False
Synpcc7942_0998 CDS 3773925 chromosome 1005621 1007519 + membrane protease FtsH catalytic subunit (EC 3.4.24.-) (IMGterm) False
Synpcc7942_1340 def CDS 3775533 chromosome 1374061 1374639 - peptide deformylase (EC 3.5.1.88) (IMGterm) False
Synpcc7942_1410 CDS 3774123 chromosome 1461949 1463571 - 2-isopropylmalate synthase (EC 2.3.3.13) (IMGterm) False
Synpcc7942_1519 hisD CDS 3774943 chromosome 1570976 1572280 - histidinol dehydrogenase (EC 1.1.1.23) (IMGterm) False
Synpcc7942_1554 CDS 3774978 chromosome 1611260 1611853 - ATP-dependent Clp protease proteolytic subunit ClpP (EC 3.4.21.92) (IMGterm) False
Synpcc7942_1627 CDS 3775696 chromosome 1695554 1696852 - hypothetical protein False
Synpcc7942_2128 CDS 3773685 chromosome 2207506 2208081 - thioredoxin False
Synpcc7942_2129 CDS 3773686 chromosome 2208154 2208558 + iron-sulfur cluster binding protein False
Synpcc7942_2137 CDS 3773694 chromosome 2216508 2220563 + cobaltochelatase CobN subunit (EC 6.6.1.2) (IMGterm) False
Synpcc7942_2188 CDS 3773745 chromosome 2266131 2267534 - isochorismate synthase (EC:5.4.4.2) False
Synpcc7942_2365 prfC CDS 3774648 chromosome 2430839 2432509 + bacterial peptide chain release factor 3 (bRF-3) (IMGterm) False
Synpcc7942_2434 ilvH CDS 3774453 chromosome 2507663 2508181 + "acetolactate synthase, small subunit (EC 2.2.1.6) (IMGterm)" False
Synpcc7942_2446 CDS 3774465 chromosome 2523086 2523919 - "methionine aminopeptidase, type I (EC 3.4.11.18) (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_2538 CDS 3775131 chromosome 2620274 2620960 - Endopeptidase Clp (EC:3.4.21.92) False
Synpcc7942_2583 CDS 3775179 chromosome 2668299 2668931 + 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.

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.