Organism : Halobacterium salinarum NRC-1 | Module List:
Module 76 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 76

There are 7 regulatory influences for Module 76

Regulator Table (7)
Regulator Name Type
VNG1899G
VNG0536G		 combiner
VNG2476C tf
VNG1377G
VNG1816G		 combiner
VNG5028G
VNG1899G		 combiner
VNG1899G
VNG2094G		 combiner
VNG2441G
VNG2094G		 combiner
VNG0536G
VNG2476C		 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
1127 2.80e-02 AaATAtacaTcgAg
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1128 1.50e+01 gAAtcGtTTtGCG
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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 76 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 0.00e+00 0.00e+00 23/30
Two-component system kegg pathway 5.80e-05 5.26e-04 3/30
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 23/30
Signal Transduction kegg subcategory 5.80e-05 4.59e-04 3/30
Environmental Information Processing kegg category 0.00e+00 0.00e+00 26/30
Environmental Information Processing kegg category 0.00e+00 0.00e+00 24/30
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 23/30
ABC transporters kegg pathway 0.00e+00 0.00e+00 23/30
Signal Transduction kegg subcategory 5.80e-05 5.69e-04 3/30
Two-component system kegg pathway 5.80e-05 5.69e-04 3/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
transport biological_process 0.00e+00 0.00e+00 11/30
phosphate ion transport biological_process 0.00e+00 0.00e+00 6/30
cobalamin biosynthetic process biological_process 6.51e-04 1.61e-03 3/30
transporter activity molecular_function 0.00e+00 0.00e+00 9/30
inorganic phosphate transmembrane transporter activity molecular_function 0.00e+00 0.00e+00 6/30
ATP binding molecular_function 1.13e-03 2.20e-03 7/30
ATPase activity molecular_function 5.90e-05 2.02e-04 4/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Anions tigr sub1role 0.00e+00 0.00e+00 8/30
Transport and binding proteins tigr mainrole 0.00e+00 0.00e+00 10/30
Transport and binding proteins tigr mainrole 0.00e+00 0.00e+00 10/30
Anions tigr sub1role 0.00e+00 0.00e+00 8/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 1.98e-04 3.88e-03 4/30
Amino acid transport and metabolism cog subcategory 3.50e-05 9.84e-04 8/30
Inorganic ion transport and metabolism cog subcategory 0.00e+00 0.00e+00 21/30
Metabolism cog category 0.00e+00 0.00e+00 33/30
Metabolism cog category 0.00e+00 0.00e+00 28/30
Carbohydrate transport and metabolism cog subcategory 1.98e-04 4.60e-04 4/30
Amino acid transport and metabolism cog subcategory 3.50e-05 9.00e-05 8/30
Inorganic ion transport and metabolism cog subcategory 0.00e+00 0.00e+00 21/30
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 76

There are 30 genes in Module 76

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0451G phoU CDS 1447298 chromosome 347367 347990 - hypothetical protein VNG0451G True
VNG0452G pstB2 CDS 1447299 chromosome 348053 348898 - phosphate ABC transporter ATP-binding protein False
VNG0453G pstA2 CDS 1447300 chromosome 348905 350605 - phosphate ABC transporter permease False
VNG0455G pstC2 CDS 1447301 chromosome 350607 351566 - phosphate ABC transporter permease False
VNG0457G phoX CDS 1447302 chromosome 351622 352656 - phosphate ABC transporter periplasmic phosphate-binding protein False
VNG0458G prp1 CDS 1447303 chromosome 352883 353887 + phosphate regulatory protein-like protein True
VNG0535C CDS 1447363 chromosome 412027 412317 - hypothetical protein VNG0535C False
VNG1632G cbiQ CDS 1448189 chromosome 1215673 1216401 - hypothetical protein VNG1632G False
VNG1634G cbiN CDS 1448190 chromosome 1216405 1216695 - cobalt transport protein CbiN False
VNG1635G cbiM CDS 1448191 chromosome 1216692 1217354 - cobalt transport protein CbiM False
VNG2093G glnA CDS 1448542 chromosome 1536751 1538115 - hypothetical protein VNG2093G False
VNG2302G yuxL CDS 1448716 chromosome 1715785 1717809 + acylaminoacyl-peptidase False
VNG2358G appA CDS 1448759 chromosome 1765447 1767408 + oligopeptide binding protein False
VNG2359G appB CDS 1448760 chromosome 1767435 1768415 + oligopeptide ABC permease False
VNG2361G appC CDS 1448761 chromosome 1768417 1769577 + oligopeptide transport permease False
VNG2365G appF CDS 1448762 chromosome 1770599 1771921 + oligopeptide ABC transporter ATP-binding protein False
VNG2482G pstB1 CDS 1448852 chromosome 1856718 1857755 - phosphate ABC transporter ATP-binding protein False
VNG2483G pstA1 CDS 1448853 chromosome 1857748 1859352 - phosphate ABC transporter permease False
VNG2484G pstC1 CDS 1448854 chromosome 1859352 1860467 - phosphate transporter permease False
VNG2486G yqgG CDS 1448855 chromosome 1860511 1861650 - phosphate ABC transporter binding protein False
VNG2529G dppB2 CDS 1448894 chromosome 1897064 1898107 + hypothetical protein VNG2529G False
VNG2531G dppC1 CDS 1448895 chromosome 1898114 1899061 + dipeptide ABC transporter permease False
VNG2532H CDS 1448896 chromosome 1899063 1899422 + hypothetical protein VNG2532H False
VNG6262G zurM CDS 1449156 pNRC200 202141 203145 - ABC transporter permease False
VNG6264G zurA CDS 1449157 pNRC200 203145 203921 - ABC transporter ATP-binding protein False
VNG6265G ycdH CDS 1449158 pNRC200 203903 204952 - adhesion protein False
VNG6277G ugpB CDS 1449166 pNRC200 213229 214620 + glycerol-3-phosphate-binding protein False
VNG6279G ugpA CDS 1449167 pNRC200 214632 215525 + sn-glycerol-3-phosphate transport system permease False
VNG6280G ugpE CDS 1449168 pNRC200 215515 216393 + sn-glycerol-3-phosphate transport system permease False
VNG6281G ugpC CDS 1449169 pNRC200 216399 217538 + sn-glycerol-3-phosphate transport system ATP-binding 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.