Organism : Halobacterium salinarum NRC-1 | Module List:
Module 260 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 260

There are 3 regulatory influences for Module 260

Regulator Table (3)
Regulator Name Type
VNG5144H
VNG2614H		 combiner
VNG0996G
VNG2614H		 combiner
VNG6438G
VNG2614H		 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
1453 1.20e+04 atATtcAAG
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1454 4.60e+03 CacgG.cTg.tCGAcg.ccAagA
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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 260 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Purine metabolism kegg pathway 2.60e-05 2.80e-04 5/30
Riboflavin metabolism kegg pathway 0.00e+00 5.00e-06 3/30
Metabolic pathways kegg pathway 1.28e-04 9.35e-04 12/30
Biosynthesis of secondary metabolites kegg pathway 3.27e-04 1.69e-03 7/30
Nucleotide Metabolism kegg subcategory 8.56e-04 4.60e-03 5/30
Metabolism of Cofactors and Vitamins kegg subcategory 3.35e-04 2.13e-03 5/30
Metabolism kegg subcategory 0.00e+00 0.00e+00 21/30
Metabolism kegg category 0.00e+00 0.00e+00 24/30
Global kegg category 0.00e+00 0.00e+00 21/30
Metabolism kegg category 3.00e-04 1.98e-03 12/30
Nucleotide Metabolism kegg subcategory 1.58e-04 1.27e-03 5/30
Purine metabolism kegg pathway 2.60e-05 2.91e-04 5/30
Metabolism of Cofactors and Vitamins kegg subcategory 3.35e-04 2.13e-03 5/30
Riboflavin metabolism kegg pathway 0.00e+00 4.00e-06 3/30
Global kegg category 1.78e-04 1.38e-03 12/30
Metabolism kegg subcategory 1.78e-04 1.38e-03 12/30
Metabolic pathways kegg pathway 1.28e-04 1.07e-03 12/30
Biosynthesis of secondary metabolites kegg pathway 3.27e-04 2.09e-03 7/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Nucleotide transport and metabolism cog subcategory 3.90e-05 1.10e-03 5/30
Coenzyme transport and metabolism cog subcategory 7.57e-03 4.31e-02 4/30
Metabolism cog category 6.10e-04 9.45e-03 16/30
Metabolism cog category 2.36e-04 4.98e-04 16/30
Nucleotide transport and metabolism cog subcategory 3.90e-05 1.02e-04 5/30
Coenzyme transport and metabolism cog subcategory 7.57e-03 1.25e-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 260

There are 30 genes in Module 260

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0414G purH CDS 1447269 chromosome 321793 323580 - hypothetical protein VNG0414G False
VNG0537C CDS 1447365 chromosome 413539 416253 - hypothetical protein VNG0537C False
VNG0574C CDS 1447393 chromosome 442210 442467 + hypothetical protein VNG0574C False
VNG0628G gdhA1 CDS 1447437 chromosome 478615 479733 + glutamate dehydrogenase False
VNG0864G purL CDS 1447616 chromosome 652034 654136 - phosphoribosylformylglycinamidine synthase II False
VNG0897G rbsC1 CDS 1447639 chromosome 680470 681555 - ribose ABC transporter permease False
VNG1068G tot CDS 1447773 chromosome 815317 818580 + transmembrane oligosaccharyl transferase False
VNG1215G pai1 CDS 1447882 chromosome 916393 916875 - sporulation regulator-like protein True
VNG1305G purD CDS 1447949 chromosome 975273 976565 + hypothetical protein VNG1305G False
VNG1416G folD CDS 1448032 chromosome 1055397 1056290 + bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase False
VNG1422H CDS 1448036 chromosome 1059075 1059986 + hypothetical protein VNG1422H False
VNG1466H CDS 1448070 chromosome 1088744 1088878 + hypothetical protein VNG1466H False
VNG1533H CDS 1448120 chromosome 1141390 1143534 + hypothetical protein VNG1533H False
VNG1585Cm CDS 1449051 chromosome 1183163 1184704 - hypothetical protein VNG1585Cm False
VNG1618H CDS 1448176 chromosome 1204023 1204607 - hypothetical protein VNG1618H False
VNG1847G pchA CDS 1448355 chromosome 1364265 1365500 + potassium channel-like protein False
VNG1926G pdhA1 CDS 1448416 chromosome 1421211 1422179 - pyruvate dehydrogenase alpha subunit False
VNG1939G hemH CDS 1448425 chromosome 1429637 1430680 + phosphoribosylaminoimidazole-succinocarboxamide synthase False
VNG1940H CDS 1448426 chromosome 1430826 1431071 + hypothetical protein VNG1940H False
VNG2020C CDS 1448488 chromosome 1492979 1493509 - hypothetical protein VNG2020C True
VNG2042H CDS 1448505 chromosome 1505691 1505888 + hypothetical protein VNG2042H False
VNG2063G aca CDS 1448520 chromosome 1516948 1518180 + acetyl-CoA acetyltransferaseACA False
VNG2125Gm ribB CDS 1449061 chromosome 1563368 1564036 - 3,4-dihydroxy-2-butanone 4-phosphate synthase False
VNG2126C CDS 1448570 chromosome 1564023 1564751 - hypothetical protein VNG2126C True
VNG2371C CDS 1448769 chromosome 1777089 1777673 + IMP cyclohydrolase False
VNG2449G pepB2 CDS 1448830 chromosome 1837127 1838236 + aminopeptidase-like protein False
VNG2525H CDS 1448891 chromosome 1891808 1892323 - hypothetical protein VNG2525H False
VNG2549C CDS 1448908 chromosome 1911770 1912900 + hypothetical protein VNG2549C False
VNG2624G ribC CDS 1448965 chromosome 1963879 1964535 + riboflavin synthase subunit alpha False
VNG6308G gltP CDS 1449189 pNRC200 237796 239271 - proton/sodium-glutamate symport 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.

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.