Organism : Halobacterium salinarum NRC-1 | Module List:
Module 255 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 255

There are 4 regulatory influences for Module 255

Regulator Table (4)
Regulator Name Type
VNG0254G tf
VNG5028G
VNG0751C		 combiner
VNG0751C tf
VNG2441G
VNG0751C		 combiner

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
1443 6.20e+01 ACaCCGacgaC
Loader icon
1444 5.90e+03 GcTTTtaCG.G
Loader icon
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 255 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Fructose and mannose metabolism kegg pathway 1.00e-06 1.20e-05 3/30
Amino sugar and nucleotide sugar metabolism kegg pathway 1.50e-05 1.69e-04 3/30
Metabolic pathways kegg pathway 7.79e-03 1.52e-02 9/30
Biosynthesis of secondary metabolites kegg pathway 1.86e-03 5.73e-03 6/30
Carbohydrate Metabolism kegg subcategory 7.20e-05 5.52e-04 8/30
Replication and Repair kegg subcategory 4.80e-04 2.82e-03 3/30
Metabolism kegg subcategory 3.80e-05 3.30e-04 17/30
Metabolism kegg category 7.26e-03 2.85e-02 15/30
Genetic Information Processing kegg category 1.08e-03 5.41e-03 7/30
Global kegg category 3.80e-05 2.61e-04 17/30
Metabolism kegg category 4.39e-03 1.35e-02 10/30
Carbohydrate Metabolism kegg subcategory 4.31e-04 2.63e-03 5/30
Fructose and mannose metabolism kegg pathway 1.00e-06 1.10e-05 3/30
Amino sugar and nucleotide sugar metabolism kegg pathway 1.50e-05 1.73e-04 3/30
Nucleotide Metabolism kegg subcategory 9.96e-03 2.47e-02 3/30
Genetic Information Processing kegg category 1.44e-02 3.24e-02 5/30
Translation kegg subcategory 2.57e-02 4.94e-02 3/30
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 7.79e-03 2.04e-02 9/30
Biosynthesis of secondary metabolites kegg pathway 1.86e-03 7.50e-03 6/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
carbohydrate metabolic process biological_process 9.00e-06 5.30e-05 3/30
regulation of transcription, DNA-dependent biological_process 1.42e-02 1.88e-02 3/30
zinc ion binding molecular_function 1.42e-03 2.64e-03 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 4.07e-04 2.88e-03 3/30
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 4.07e-04 6.96e-04 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Phosphomannomutase cog 0.00e+00 0.00e+00 3/30
Carbohydrate transport and metabolism cog subcategory 2.20e-03 2.04e-02 3/30
Nucleotide transport and metabolism cog subcategory 4.19e-03 3.04e-02 3/30
Carbohydrate transport and metabolism cog subcategory 2.20e-03 3.92e-03 3/30
Nucleotide transport and metabolism cog subcategory 4.19e-03 7.22e-03 3/30
Phosphomannomutase cog 0.00e+00 0.00e+00 3/30
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 255

There are 30 genes in Module 255

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0132C CDS 1447059 chromosome 109834 110448 - hypothetical protein VNG0132C False
VNG0133G rpa CDS 1447061 chromosome 110769 112193 + replication factor A False
VNG0361C CDS 1447232 chromosome 284272 285273 + hypothetical protein VNG0361C False
VNG0439C CDS 1447288 chromosome 338014 339384 - hypothetical protein VNG0439C False
VNG0896G cda CDS 1447638 chromosome 680015 680419 - cytidine deaminase False
VNG0905G pmu2 CDS 1447643 chromosome 685465 686847 - phosphomannomutase False
VNG1297C CDS 1447943 chromosome 968577 969803 + S-adenosylmethionine synthetase False
VNG1356G fumC CDS 1447987 chromosome 1011395 1012807 - fumarate hydratase False
VNG1367G srp19 CDS 1447995 chromosome 1017722 1018000 - signal recognition particle False
VNG1377G asnC CDS 1448002 chromosome 1026961 1027410 - transcription regulator True
VNG1442G htr12 CDS 1448050 chromosome 1069113 1070375 - Htr12 False
VNG1493G purF CDS 1448093 chromosome 1108559 1110031 - hypothetical protein VNG1493G False
VNG1874C CDS 1448375 chromosome 1385685 1386209 + hypothetical protein VNG1874C False
VNG1877C CDS 1448377 chromosome 1387529 1387846 + hypothetical protein VNG1877C False
VNG1999H CDS 1448473 chromosome 1477154 1477636 - hypothetical protein VNG1999H False
VNG2010G rps19e CDS 1448481 chromosome 1485424 1485879 - 30S ribosomal protein S19e False
VNG2015C pyrH CDS 1448485 chromosome 1488724 1489449 + uridylate kinase False
VNG2021C CDS 1448489 chromosome 1493620 1495098 + hypothetical protein VNG2021C False
VNG2072G serS CDS 1448526 chromosome 1524446 1525828 + seryl-tRNA synthetase False
VNG2206G pmu1 CDS 1448638 chromosome 1635310 1636677 + phosphomannomutase False
VNG2276G pmm CDS 1448693 chromosome 1694075 1695448 + phosphoglucomutase/phospho-mannomutase False
VNG2333C CDS 1448741 chromosome 1739430 1740857 + hypothetical protein VNG2333C False
VNG2504G pheS CDS 1448866 chromosome 1869757 1871265 + phenylalanyl-tRNA synthetase subunit alpha False
VNG2598G hisH1 CDS 1448946 chromosome 1942737 1943348 - glutamine amidotransferase subunit PdxT False
VNG2643H CDS 1448982 chromosome 1980191 1980583 + hypothetical protein VNG2643H False
VNG6260G ftsZ5 CDS 1449154 pNRC200 199555 200640 + cell division protein False
VNG6268C CDS 1449160 pNRC200 206380 208347 + hypothetical protein VNG6268C False
VNG6420H CDS 1449399 pNRC200 322488 323033 - hypothetical protein VNG6420H False
VNG7006 CDS 1446808 pNRC100 4215 4610 + hypothetical protein VNG7006 False
VNG7007 CDS 1446809 pNRC100 4614 4811 + hypothetical protein VNG7007 True

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.