Organism : Halobacterium salinarum NRC-1 | Module List:
Module 118 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 118

There are 2 regulatory influences for Module 118

Regulator Table (2)
Regulator Name Type
VNG0462C tf
VNG1886C tf

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 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
1209 2.40e-01 CGAcctCGgcG
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1210 2.20e+04 t.aC.gTgagctAgCC.aca
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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 118 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 2.00e-06 5/30
Biosynthesis of secondary metabolites kegg pathway 8.84e-03 1.68e-02 5/30
Lipid Metabolism kegg subcategory 7.52e-04 4.14e-03 3/30
Amino Acid Metabolism kegg subcategory 0.00e+00 1.00e-06 12/30
Metabolism kegg subcategory 1.93e-02 4.74e-02 12/30
Metabolism kegg category 2.44e-03 1.12e-02 16/30
Amino Acid Metabolism kegg subcategory 3.08e-03 1.05e-02 5/30
Phenylalanine tyrosine and tryptophan biosynthesis kegg pathway 0.00e+00 2.00e-06 5/30
Biosynthesis of secondary metabolites kegg pathway 8.84e-03 2.26e-02 5/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
tryptophan metabolic process biological_process 0.00e+00 0.00e+00 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 2.42e-04 4.42e-03 7/30
Metabolism cog category 2.36e-02 3.61e-02 12/30
Poorly characterized cog category 5.26e-03 8.88e-03 10/30
Amino acid transport and metabolism cog subcategory 2.42e-04 5.10e-04 7/30
Function unknown cog subcategory 1.29e-02 2.08e-02 5/30
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 118

There are 30 genes in Module 118

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0025H CDS 1446971 chromosome 20219 20482 - hypothetical protein VNG0025H False
VNG0170Cm CDS 1449011 chromosome 144354 144983 - polyketide biosynthesis dithiol-disulfide isomerase False
VNG0205H CDS 1447123 chromosome 173537 173824 - hypothetical protein VNG0205H False
VNG0268C CDS 1447170 chromosome 216982 218070 + hypothetical protein VNG0268C False
VNG0284C CDS 1447180 chromosome 227135 228829 + hypothetical protein VNG0284C False
VNG0300C CDS 1447190 chromosome 236318 237037 - hypothetical protein VNG0300C False
VNG0305G trpC CDS 1447194 chromosome 240541 241296 + hypothetical protein VNG0305G False
VNG0307G trpB CDS 1447195 chromosome 241293 242585 + tryptophan synthase subunit beta False
VNG0308Gm trpA CDS 1449015 chromosome 242582 243412 + tryptophan synthase subunit alpha False
VNG0314G aroD CDS 1447200 chromosome 246267 246854 - 3-dehydroquinate dehydratase False
VNG0318G dpg CDS 1447203 chromosome 248973 250817 - dolichol-P-glucose synthetase False
VNG0346H CDS 1447223 chromosome 274440 274601 - hypothetical protein VNG0346H False
VNG0364G yusZ3 CDS 1447234 chromosome 286131 286952 + oxidoreductase False
VNG0367H CDS 1447236 chromosome 288101 288445 + hypothetical protein VNG0367H False
VNG0378C CDS 1447243 chromosome 293888 295060 - hypothetical protein VNG0378C False
VNG0502G aspB1 CDS 1447337 chromosome 388169 389290 + aspartate aminotransferase False
VNG0777G taqD CDS 1447551 chromosome 584205 584645 - glycerol-3-phosphate cytidyltransferase False
VNG0799C CDS 1447568 chromosome 601488 602189 + hypothetical protein VNG0799C False
VNG0908G putP CDS 1447646 chromosome 687787 689355 + hypothetical protein VNG0908G False
VNG0914H CDS 1447650 chromosome 691613 692713 - hypothetical protein VNG0914H False
VNG1341G fabG CDS 1447977 chromosome 1000227 1000994 + 3-oxoacyl- False
VNG1382H CDS 1448007 chromosome 1030300 1030734 + hypothetical protein VNG1382H False
VNG1869C CDS 1448371 chromosome 1380897 1382075 - hypothetical protein VNG1869C False
VNG1896C CDS 1448391 chromosome 1402807 1404606 + hypothetical protein VNG1896C False
VNG1957G tgtA2 CDS 1448440 chromosome 1444126 1445883 - archaeosine tRNA-ribosyltransferase False
VNG1974H CDS 1448452 chromosome 1458039 1458560 + hypothetical protein VNG1974H False
VNG1989H CDS 1448465 chromosome 1470434 1470907 - hypothetical protein VNG1989H False
VNG2003G truA CDS 1448477 chromosome 1482219 1483019 - tRNA pseudouridine synthase A False
VNG6052H CDS 1449214 pNRC200 41210 41368 - hypothetical protein VNG6052H False
VNG6189H CDS 1449104 pNRC200 160682 161470 + hypothetical protein VNG6189H 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 118

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.