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

GeneModule member RegulatorRegulator MotifMotif
Cytoscape Web
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 1

There are 4 regulatory influences for Module 1

Regulator Table (4)
Regulator Name Type
VNG0101G tf
VNG2661G tf
VNG0315G tf
VNG0374G
VNG0315G
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
981 4.00e-01 TTCGACgc.Tttct
Loader icon
982 1.50e+04 TCaTGATGAA
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 1 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 9.24e-03 1.74e-02 3/40
Pyrimidine metabolism kegg pathway 5.22e-03 1.12e-02 3/40
RNA polymerase kegg pathway 9.90e-05 8.06e-04 3/40
Ribosome kegg pathway 0.00e+00 0.00e+00 31/40
Nucleotide Metabolism kegg subcategory 7.30e-04 4.07e-03 6/40
Transcription kegg subcategory 1.25e-03 6.06e-03 3/40
Translation kegg subcategory 0.00e+00 0.00e+00 31/40
Genetic Information Processing kegg category 0.00e+00 0.00e+00 36/40
Purine metabolism kegg pathway 9.24e-03 2.34e-02 3/40
Pyrimidine metabolism kegg pathway 5.22e-03 1.52e-02 3/40
Genetic Information Processing kegg category 0.00e+00 0.00e+00 36/40
Transcription kegg subcategory 1.25e-03 5.76e-03 3/40
RNA polymerase kegg pathway 9.90e-05 8.90e-04 3/40
Translation kegg subcategory 0.00e+00 0.00e+00 31/40
Ribosome kegg pathway 0.00e+00 0.00e+00 31/40

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
translation biological_process 0.00e+00 0.00e+00 30/40
RNA binding molecular_function 7.36e-04 1.50e-03 3/40
structural constituent of ribosome molecular_function 0.00e+00 0.00e+00 31/40
DNA-directed RNA polymerase activity molecular_function 1.84e-04 5.47e-04 3/40
DNA-directed RNA polymerase I activity molecular_function 1.84e-04 5.47e-04 3/40
DNA-directed RNA polymerase II activity molecular_function 1.84e-04 5.47e-04 3/40
DNA-directed RNA polymerase III activity molecular_function 1.84e-04 5.47e-04 3/40

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 14/40
Protein synthesis tigr mainrole 0.00e+00 0.00e+00 14/40
Protein synthesis tigr mainrole 0.00e+00 0.00e+00 14/40
Ribosomal proteins: synthesis and modification tigr sub1role 0.00e+00 0.00e+00 14/40

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 0.00e+00 31/40
Information storage and processing cog category 0.00e+00 0.00e+00 34/40
Information storage and processing cog category 0.00e+00 0.00e+00 34/40
Translation, ribosomal structure and biogenesis cog subcategory 0.00e+00 0.00e+00 31/40
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 1

There are 40 genes in Module 1

Gene Member Table (40)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0548C CDS 1447373 chromosome 422662 422844 - H/ACA RNA-protein complex component Nop10p False
VNG0550G rps27e CDS 1447375 chromosome 423644 423817 - 30S ribosomal protein S27e False
VNG0551G rpl44e CDS 1447376 chromosome 423822 424007 - 50S ribosomal protein L44E False
VNG1103G rpl12p CDS 1447799 chromosome 845055 845399 - 50S ribosomal protein L12P False
VNG1104G rplP0 CDS 1447800 chromosome 845405 846463 - acidic ribosomal protein P0 False
VNG1105G rpl1P CDS 1447801 chromosome 846465 847103 - 50S ribosomal protein L1P False
VNG1108G rpl11p CDS 1447802 chromosome 847304 847795 - 50S ribosomal protein L11P False
VNG1111G drg CDS 1447804 chromosome 848173 849285 + GTP-binding protein DRG False
VNG1114G glo1 CDS 1447806 chromosome 849749 850534 + glyoxalase False
VNG1132G rps13p CDS 1447819 chromosome 860275 860790 + 30S ribosomal protein S13P False
VNG1133G rps4p CDS 1447820 chromosome 860790 861302 + 30S ribosomal protein S4P False
VNG1134G rps11p CDS 1447821 chromosome 861309 861692 + 30S ribosomal protein S11P False
VNG1136G rpb3 CDS 1447822 chromosome 861696 862442 + DNA-directed RNA polymerase II False
VNG1137G rpl18e CDS 1447824 chromosome 862694 863047 + 50S ribosomal protein L18e False
VNG1138G rpl13p CDS 1447825 chromosome 863044 863481 + 50S ribosomal protein L13P False
VNG1139Gm rps9p CDS 1449037 chromosome 863475 863873 + 30S ribosomal protein S9P False
VNG1140G rpoN CDS 1447826 chromosome 863886 864086 + DNA-directed RNA polymerase subunit N False
VNG1141G rpoK CDS 1447827 chromosome 864089 864271 + DNA-directed RNA polymerase subunit K False
VNG1142G eno CDS 1447828 chromosome 864273 865469 + phosphopyruvate hydratase False
VNG1143G rps2P CDS 1447829 chromosome 865466 866215 + 30S ribosomal protein S2 False
VNG1689G rpl3p CDS 1448237 chromosome 1259033 1260040 + 50S ribosomal protein L3P False
VNG1690G rpl4lp CDS 1448238 chromosome 1260044 1260796 + 50S ribosomal protein L4P False
VNG1691G rplW CDS 1448239 chromosome 1260793 1261047 + 50S ribosomal protein L23P False
VNG1692G rpl2p CDS 1448240 chromosome 1261050 1261772 + 50S ribosomal protein L2P False
VNG1693G rps19p CDS 1448241 chromosome 1261776 1262198 + 30S ribosomal protein S19P False
VNG1695G rpl22p CDS 1448242 chromosome 1262202 1262672 + 50S ribosomal protein L22P False
VNG1697G rps3p CDS 1448243 chromosome 1262672 1263580 + 30S ribosomal protein S3P False
VNG1699C CDS 1448245 chromosome 1263804 1264175 + ribonuclease P protein component 1 False
VNG1700G rps17p CDS 1448246 chromosome 1264166 1264495 + 30S ribosomal protein S17P False
VNG1701G rpl14p CDS 1448247 chromosome 1264495 1264893 + 50S ribosomal protein L14P False
VNG1702G rpl24p CDS 1448248 chromosome 1264898 1265254 + 50S ribosomal protein L24P False
VNG1705G rpl5p CDS 1448250 chromosome 1265949 1266476 + 50S ribosomal protein L5P False
VNG1707G rps8p CDS 1448252 chromosome 1266634 1267026 + 30S ribosomal protein S8P False
VNG1709G rpl6p CDS 1448253 chromosome 1267030 1267566 + 50S ribosomal protein L6P False
VNG1713G rpl19e CDS 1448255 chromosome 1268282 1268731 + 50S ribosomal protein L19e False
VNG1718G rpl15p CDS 1448259 chromosome 1270394 1270855 + 50S ribosomal protein L15P False
VNG1719G secY CDS 1448260 chromosome 1270859 1272334 + preprotein translocase subunit SecY False
VNG2467G rpl31e CDS 1448841 chromosome 1846287 1846565 - 50S ribosomal protein L31e False
VNG2469G rpl39e CDS 1448842 chromosome 1846565 1846717 - 50S ribosomal protein L39e False
VNG2514G rps6e CDS 1448881 chromosome 1885376 1885771 + 30S ribosomal protein S6e 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.

Comments for Module 1

Please add your comments for this module by using the form below. Your comments will be publicly available.

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Social Help

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.

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.