Organism : Halobacterium salinarum NRC-1 | Module List:
Module 119 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 119

There are 0 regulatory influences for Module 119

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 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
1211 1.40e+03 ttcGgAAtat.cAtA
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1212 5.50e+03 GatCGaCggcGaCGAg.ACACcC
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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 119 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 2.34e-02 3.57e-02 8/30
Biosynthesis of secondary metabolites kegg pathway 3.48e-02 4.88e-02 4/30
Microbial metabolism in diverse environments kegg pathway 2.68e-02 3.97e-02 3/30
Carbohydrate Metabolism kegg subcategory 2.47e-03 1.03e-02 6/30
Energy Metabolism kegg subcategory 4.82e-04 2.82e-03 6/30
Metabolism kegg subcategory 6.68e-04 3.74e-03 15/30
Metabolism kegg category 1.87e-04 1.20e-03 18/30
Global kegg category 6.68e-04 3.62e-03 15/30
Metabolism kegg category 1.38e-02 3.18e-02 9/30
Carbohydrate Metabolism kegg subcategory 1.84e-02 3.90e-02 3/30
Energy Metabolism kegg subcategory 6.12e-03 1.70e-02 4/30
Global kegg category 9.73e-03 2.43e-02 9/30
Metabolism kegg subcategory 9.73e-03 2.43e-02 9/30
Metabolic pathways kegg pathway 2.34e-02 4.59e-02 8/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 3.60e-03 5.93e-03 4/30

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 119

There are 30 genes in Module 119

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0102C CDS 1447034 chromosome 84927 85583 - hypothetical protein VNG0102C False
VNG0330G ppsA CDS 1447213 chromosome 260291 262549 - phosphoenolpyruvate synthase False
VNG0404H CDS 1447261 chromosome 311391 311921 + hypothetical protein VNG0404H False
VNG0540G imp CDS 1447367 chromosome 416799 417755 - hypothetical protein VNG0540G False
VNG0578H CDS 1447396 chromosome 444728 445168 + hypothetical protein VNG0578H False
VNG0583G cyb CDS 1447400 chromosome 446666 447478 - cytochrome b6 False
VNG0684G fbp CDS 1447483 chromosome 520705 521568 + fructose-1,6-bisphosphatase False
VNG0795G hcpC CDS 1447565 chromosome 598271 598744 + halocyanin-like protein False
VNG0965C CDS 1447690 chromosome 735910 736773 - hypothetical protein VNG0965C False
VNG1309G sdhD CDS 1447952 chromosome 979298 979660 - membrane anchor False
VNG1668G rps8e CDS 1448220 chromosome 1244981 1245355 - 30S ribosomal protein S8e False
VNG1726G htlB CDS 1448265 chromosome 1276763 1277635 + HtlB False
VNG2089H CDS 1448540 chromosome 1535505 1535945 + hypothetical protein VNG2089H False
VNG2120G yusM CDS 1448565 chromosome 1557442 1558281 + proline dehydrogenase False
VNG2224G ocd1 CDS 1448652 chromosome 1654897 1655772 - ornithine cyclodeaminase False
VNG2283G alaS CDS 1448699 chromosome 1699204 1701993 + alanyl-tRNA synthetase False
VNG2339C CDS 1448746 chromosome 1750278 1750697 - hypothetical protein VNG2339C False
VNG2372G rad24c CDS 1448770 chromosome 1777719 1778402 + DNA repair protein False
VNG2402H CDS 1448794 chromosome 1802881 1802985 - hypothetical protein VNG2402H False
VNG2459G srp54 CDS 1448837 chromosome 1841954 1843336 - signal recognition particle False
VNG2472G nifU CDS 1448846 chromosome 1849321 1849749 + hypothetical protein VNG2472G False
VNG2541Cm pncB CDS 1449072 chromosome 1905159 1906304 + nicotinate phosphoribosyltransferase False
VNG2585H CDS 1448936 chromosome 1936134 1936334 + hypothetical protein VNG2585H False
VNG5123H cds None pNRC100 89038 89376 - None False
VNG6255C CDS 1449151 pNRC200 197387 197656 + hypothetical protein VNG6255C False
VNG6256G lipB CDS 1449152 pNRC200 197890 198399 + lipoate protein ligase False
VNG6309G pyrB CDS 1449190 pNRC200 239301 240326 + aspartate carbamoyltransferase catalytic subunit False
VNG6315G arcB CDS 1449194 pNRC200 244821 245708 - ornithine carbamoyltransferase False
VNG7020 gvpH CDS 1446780 pNRC100 18658 19206 - gas vesicle protein GvpH False
VNG7040 cydB CDS 1446792 pNRC100 43698 44693 + cytochrome d ubiquinol oxidase subunit II 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 119

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.