Organism : Halobacterium salinarum NRC-1 | Module List:
Module 11 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 11

There are 4 regulatory influences for Module 11

Regulator Table (4)
Regulator Name Type
VNG1123G
VNG6143H		 combiner
VNG1922G tf
VNG0651G tf
VNG6288C 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
1001 0.00e+00 acAccCAAacacaTgGgGgaTcgG
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1002 5.00e-04 AAAttGATTGcgtcctgtaGtta
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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 11 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Nicotinate and nicotinamide metabolism kegg pathway 2.00e-06 2.40e-05 3/30
Metabolism of Cofactors and Vitamins kegg subcategory 1.58e-02 4.23e-02 3/30
Metabolism of Cofactors and Vitamins kegg subcategory 1.58e-02 3.48e-02 3/30
Nicotinate and nicotinamide metabolism kegg pathway 2.00e-06 2.40e-05 3/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 2.04e-02 2.59e-02 3/30
oxidoreductase activity molecular_function 6.19e-03 9.16e-03 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 3.23e-03 1.09e-02 3/30
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 3.23e-03 4.50e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 1.71e-02 2.69e-02 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 11

There are 30 genes in Module 11

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0654C CDS 1447458 chromosome 499989 500732 - hypothetical protein VNG0654C True
VNG0656H CDS 1447459 chromosome 500787 501026 - hypothetical protein VNG0656H False
VNG0828H CDS 1447591 chromosome 627213 627452 + hypothetical protein VNG0828H False
VNG0829G dmsA CDS 1447592 chromosome 627445 629958 + dimethylsulfoxide reductase False
VNG0830G hmoA CDS 1447593 chromosome 629955 630743 + HmoA False
VNG0831G moz CDS 1447594 chromosome 630743 632050 + molybdopterin oxidoreductase False
VNG0832C CDS 1447595 chromosome 632047 632625 + hypothetical protein VNG0832C False
VNG1039H CDS 1447751 chromosome 794483 795025 + hypothetical protein VNG1039H False
VNG1370G btuC CDS 1447997 chromosome 1019209 1020318 + corrinoid ABC transporter permease False
VNG1405C CDS 1448023 chromosome 1042533 1042907 - hypothetical protein VNG1405C True
VNG1458G crtB1 CDS 1448063 chromosome 1081040 1082008 - phytoene synthase False
VNG1459H CDS 1448064 chromosome 1082119 1082265 - hypothetical protein VNG1459H False
VNG1461H CDS 1448065 chromosome 1082555 1082767 - hypothetical protein VNG1461H False
VNG1462G cdc48a CDS 1448066 chromosome 1082767 1084842 - cell division cycle protein False
VNG1463G blp CDS 1448067 chromosome 1085033 1085461 + bacterio-opsin linked protein False
VNG1464G bat CDS 1448068 chromosome 1085495 1087519 - bacterio-opsin activator True
VNG1465G brp CDS 1448069 chromosome 1087516 1088622 - bacteriorhodopsin-like protein False
VNG1467G bop CDS 1448071 chromosome 1089122 1089910 + bacterio-opsin False
VNG1468H CDS 1448072 chromosome 1089962 1090231 + hypothetical protein VNG1468H False
VNG1628G aad CDS 1448186 chromosome 1213427 1214401 - aryl-alcohol dehydrogenase False
VNG1630H CDS 1448187 chromosome 1214457 1214690 - hypothetical protein VNG1630H False
VNG1655H CDS 1448209 chromosome 1234475 1234831 - hypothetical protein VNG1655H False
VNG1656H CDS 1448211 chromosome 1235959 1236402 + hypothetical protein VNG1656H False
VNG1657H CDS 1448210 chromosome 1234828 1235829 - hypothetical protein VNG1657H False
VNG1755G crtI2 CDS 1448284 chromosome 1294848 1296458 - phytoene dehydrogenase False
VNG1882G nadA CDS 1448380 chromosome 1390684 1391808 + quinolinate synthetase False
VNG1883G nadB CDS 1448381 chromosome 1391811 1393340 + L-aspartate oxidase False
VNG1884G nadC CDS 1448382 chromosome 1393327 1394133 + hypothetical protein VNG1884G False
VNG2137G ggt CDS 1448578 chromosome 1571291 1571779 - geranylgeranyl-diphosphate geranylgeranyltransferase False
VNG2535H CDS 1448900 chromosome 1902361 1902801 + hypothetical protein VNG2535H 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.