Organism : Halobacterium salinarum NRC-1 | Module List:
Module 29 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 29

There are 3 regulatory influences for Module 29

Regulator Table (3)
Regulator Name Type
VNG2661G
VNG1029C		 combiner
VNG0194H tf
VNG0258H 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
1035 1.80e+00 Cag.AaTtaacgTttataa
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1036 3.80e+02 tTTAtaacCgt
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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 29 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Citrate cycle (TCA cycle) kegg pathway 1.09e-04 8.57e-04 3/26
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 9/26
Carbon fixation pathways in prokaryotes kegg pathway 1.93e-04 1.26e-03 3/26
Metabolic pathways kegg pathway 0.00e+00 7.00e-06 14/26
Microbial metabolism in diverse environments kegg pathway 2.69e-03 7.16e-03 4/26
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 13/26
Amino Acid Metabolism kegg subcategory 8.68e-03 2.58e-02 5/26
Metabolism kegg subcategory 0.00e+00 0.00e+00 21/26
Metabolism kegg category 0.00e+00 0.00e+00 24/26
Global kegg category 0.00e+00 0.00e+00 21/26
Metabolism kegg category 0.00e+00 3.00e-06 15/26
Carbohydrate Metabolism kegg subcategory 1.12e-02 2.70e-02 3/26
Citrate cycle (TCA cycle) kegg pathway 1.09e-04 9.55e-04 3/26
Energy Metabolism kegg subcategory 0.00e+00 0.00e+00 13/26
Oxidative phosphorylation kegg pathway 0.00e+00 0.00e+00 9/26
Carbon fixation pathways in prokaryotes kegg pathway 1.93e-04 1.47e-03 3/26
Global kegg category 1.00e-06 1.00e-05 14/26
Metabolism kegg subcategory 1.00e-06 1.00e-05 14/26
Metabolic pathways kegg pathway 0.00e+00 7.00e-06 14/26
Microbial metabolism in diverse environments kegg pathway 2.69e-03 9.54e-03 4/26

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
electron transport biological_process 1.86e-03 3.50e-03 4/26
mitochondrial electron transport, NADH to ubiquinone biological_process 0.00e+00 0.00e+00 5/26
NADH dehydrogenase (ubiquinone) activity molecular_function 0.00e+00 0.00e+00 9/26

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Electron transport tigr sub1role 0.00e+00 3.00e-06 3/26
Energy metabolism tigr mainrole 3.00e-06 5.50e-05 5/26
Energy metabolism tigr mainrole 3.00e-06 6.00e-06 5/26
Electron transport tigr sub1role 0.00e+00 1.00e-06 3/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 11/26
Metabolism cog category 5.00e-05 1.19e-03 16/26
Metabolism cog category 4.28e-04 8.57e-04 14/26
Energy production and conversion cog subcategory 0.00e+00 0.00e+00 11/26
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 29

There are 26 genes in Module 29

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0208H CDS 1447125 chromosome 175471 175920 + hypothetical protein VNG0208H False
VNG0209H CDS 1447126 chromosome 175913 176947 + hypothetical protein VNG0209H False
VNG0635G nolB CDS 1447443 chromosome 485194 485604 + NADH dehydrogenase/oxidoreductase-like protein False
VNG0636G ndhG1 CDS 1447444 chromosome 485597 486304 + NADH dehydrogenase/oxidoreductase False
VNG0637G ndhG5 CDS 1447445 chromosome 486301 487989 + NADH dehydrogenase/oxidoreductase False
VNG0639G ndhG4 CDS 1447446 chromosome 488101 489045 + NADH dehydrogenase/oxidoreductase False
VNG0640G nolD CDS 1447447 chromosome 489042 489503 + NADH dehydrogenase/oxidoreductase-like protein False
VNG0641C CDS 1447448 chromosome 489561 489821 + NADH dehydrogenase subunit J False
VNG0642C CDS 1447449 chromosome 489893 490126 + hypothetical protein VNG0642C False
VNG0643G nolC CDS 1447450 chromosome 490126 490428 + NADH dehydrogenase/oxidoreductase-like protein False
VNG0646G nuoL CDS 1447451 chromosome 490430 492508 + F420H2:quinone oxidoreductase subunit L False
VNG0940Gm ACS3 CDS 1449030 chromosome 716669 718771 + Acetyl-CoA synthetase False
VNG1125G korB CDS 1447814 chromosome 855719 856657 - KorB False
VNG1128G korA CDS 1447815 chromosome 856660 858582 - KorA False
VNG2122G ilvE2 CDS 1448567 chromosome 1559008 1559934 - branched-chain amino acid aminotransferase False
VNG2226G cctA CDS 1448653 chromosome 1656061 1657806 - thermosome subunit alpha False
VNG2243G tbpE CDS 1448667 chromosome 1670410 1670970 + transcription factor True
VNG2244H CDS 1448668 chromosome 1670977 1671342 + hypothetical protein VNG2244H False
VNG2251G achY CDS 1448673 chromosome 1674660 1675943 + S-adenosyl-L-homocysteine hydrolase False
VNG2337C CDS 1448744 chromosome 1745788 1746138 + hypothetical protein VNG2337C False
VNG2539H CDS 1448902 chromosome 1903499 1905028 + hypothetical protein VNG2539H False
VNG2574G can CDS 1448927 chromosome 1930439 1932424 + aconitate hydratase False
VNG2648G rps10p CDS 1448988 chromosome 1984401 1984709 - 30S ribosomal protein S10P False
VNG2649G eef1a CDS 1448989 chromosome 1984713 1985978 - elongation factor 1-alpha False
VNG6294G perA CDS 1449179 pNRC200 225010 227172 - peroxidase / catalase False
VNG6312G argS CDS 1449192 pNRC200 240914 242809 + arginine-tRNA synthetase 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.