Organism : Synechococcus elongatus PCC 7942 | Module List:
Module 124 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 124

There are 0 regulatory influences for Module 124

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
1889 4.40e-02 ATTTgaGa.cTaAa.CAaGTC
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1890 1.30e+00 CAaTttTG
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1891 4.30e-01 gaTgctttAcagTtctT.AttT
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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 124 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 3.48e-03 4.82e-02 4/32
Information storage and processing cog category 9.81e-03 1.69e-02 8/32
Transcription cog subcategory 3.48e-03 6.29e-03 4/32
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 124

There are 32 genes in Module 124

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
Synpcc7942_0040 CDS 3775752 chromosome 38630 39007 + dihydroneopterin aldolase Dihydroneopterin aldolase (EC:4.1.2.25) False
Synpcc7942_0120 CDS 3773460 chromosome 119508 119993 - Cytosine/adenosine deaminase-like False
Synpcc7942_0526 CDS 3774764 chromosome 510412 511293 + "carbohydrate ABC transporter membrane protein 1, CUT1 family (TC 3.A.1.1.-) (IMGterm)" False
Synpcc7942_0650 CDS 3775633 chromosome 644174 644659 - hypothetical protein False
Synpcc7942_0651 CDS 3775634 chromosome 644741 647161 + replication restart DNA helicase PriA (IMGterm) False
Synpcc7942_0672 CDS 3775655 chromosome 666887 667849 + group2 RNA polymerase sigma factor SigD True
Synpcc7942_0914 CDS 3774092 chromosome 921780 922391 - tRNA-(MS(2)IO(6)A)-hydroxylase-like (EC:1.-) False
Synpcc7942_1111 CDS 3775061 chromosome 1127864 1129447 - serine/threonine protein kinase (IMGterm) False
Synpcc7942_1112 CDS 3775062 chromosome 1129444 1130385 - ribosomal large subunit pseudouridine synthase D (EC 5.4.99.-) (IMGterm) False
Synpcc7942_1243 CDS 3773531 chromosome 1267422 1268117 - cyclic nucleotide-binding domain (cNMP-BD) protein False
Synpcc7942_1299 CDS 3773588 chromosome 1326892 1327854 - hypothetical protein False
Synpcc7942_1300 CDS 3773589 chromosome 1328093 1328662 + 5-formyltetrahydrofolate cyclo-ligase (IMGterm) False
Synpcc7942_1336 CDS 3775529 chromosome 1367261 1368343 + hypothetical protein False
Synpcc7942_1337 CDS 3775530 chromosome 1368411 1372715 + Integrins alpha chain False
Synpcc7942_1360 CDS 3775553 chromosome 1399742 1401052 + cell envelope-related transcriptional attenuator (IMGterm) True
Synpcc7942_1468 CDS 3773640 chromosome 1521482 1522141 - "multisubunit sodium/proton antiporter, MrpB subunit (TC 2.A.63.1) (IMGterm)" False
Synpcc7942_1558 CDS 3774982 chromosome 1615204 1616271 + hypothetical protein False
Synpcc7942_1599 CDS 3775023 chromosome 1665097 1666182 + hypothetical protein False
Synpcc7942_1604 CDS 3775671 chromosome 1669273 1670625 + hypothetical protein False
Synpcc7942_1706 CDS 3775405 chromosome 1773234 1775426 + hypothetical protein False
Synpcc7942_1739 CDS 3775439 chromosome 1809717 1810142 + "transcriptional regulator, MerR family (IMGterm)" True
Synpcc7942_1740 CDS 3775440 chromosome 1810183 1811088 - UDP-N-acetylmuramate dehydrogenase (EC 1.1.1.158) (IMGterm) False
Synpcc7942_1788 CDS 3774363 chromosome 1855204 1859910 + hypothetical protein False
Synpcc7942_1869 CDS 3775232 chromosome 1938280 1941534 - probable cation efflux system protein False
Synpcc7942_1889 CDS 3775252 chromosome 1961987 1963582 - (1->4)-alpha-D-glucan branching enzyme (IMGterm) False
Synpcc7942_1893 CDS 3775256 chromosome 1965754 1966530 - neutral amino acid ABC transporter ATP-binding protein (IMGterm) False
Synpcc7942_2000 CDS 3774187 chromosome 2067958 2070180 - Penicillin-binding protein 1A (EC:2.4.1.129) False
Synpcc7942_2012 CDS 3774199 chromosome 2081506 2082729 + stage II sporulation protein D-like False
Synpcc7942_2237 CDS 3773893 chromosome 2303053 2303487 - hypothetical protein False
Synpcc7942_2414 CDS 3774698 chromosome 2485595 2486650 - hypothetical protein False
Synpcc7942_2464 CDS 3774484 chromosome 2545468 2546166 - N-acylglucosamine-6-phosphate 2-epimerase (EC:5.1.3.9) False
Synpcc7942_2528 CDS 3775121 chromosome 2609741 2610427 + 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 124

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.