Organism : Halobacterium salinarum NRC-1 | Module List:
Module 191 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 191

There are 3 regulatory influences for Module 191

Regulator Table (3)
Regulator Name Type
VNG0258H tf
VNG2661G
VNG1029C		 combiner
VNG2243G 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
1337 4.80e+02 tcgacTgtcTc.gcGtTgt
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1338 2.90e+04 ATTGAAA
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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 191 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Biosynthesis of secondary metabolites kegg pathway 8.84e-03 1.68e-02 5/30
Microbial metabolism in diverse environments kegg pathway 5.17e-03 1.11e-02 4/30
Carbohydrate Metabolism kegg subcategory 2.47e-03 1.03e-02 6/30
Amino Acid Metabolism kegg subcategory 8.94e-04 4.70e-03 7/30
Metabolism of Cofactors and Vitamins kegg subcategory 1.58e-02 4.23e-02 3/30
Xenobiotics Biodegradation and Metabolism kegg subcategory 7.60e-05 5.78e-04 3/30
Replication and Repair kegg subcategory 1.00e-06 1.50e-05 5/30
Metabolism kegg subcategory 1.70e-04 1.18e-03 16/30
Metabolism kegg category 0.00e+00 0.00e+00 28/30
Genetic Information Processing kegg category 3.00e-05 2.12e-04 9/30
Global kegg category 1.70e-04 1.11e-03 16/30
Metabolism kegg category 1.38e-02 3.18e-02 9/30
Metabolism of Cofactors and Vitamins kegg subcategory 1.58e-02 3.48e-02 3/30
Xenobiotics Biodegradation and Metabolism kegg subcategory 4.30e-05 4.52e-04 3/30
Genetic Information Processing kegg category 3.37e-03 1.11e-02 6/30
Biosynthesis of secondary metabolites kegg pathway 8.84e-03 2.26e-02 5/30
Microbial metabolism in diverse environments kegg pathway 5.17e-03 1.50e-02 4/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
oxidoreductase activity molecular_function 6.19e-03 9.16e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 2.24e-03 2.05e-02 4/30
Transcription cog subcategory 2.92e-02 4.36e-02 3/30
Posttranslational modification, protein turnover, chaperones cog subcategory 2.24e-03 3.98e-03 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 191

There are 30 genes in Module 191

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0101G cspD1 CDS 1447033 chromosome 84617 84841 - cold shock protein True
VNG0130H CDS 1447058 chromosome 109649 109831 + hypothetical protein VNG0130H False
VNG0233H CDS 1447145 chromosome 196042 196281 - hypothetical protein VNG0233H False
VNG0283C CDS 1447178 chromosome 225590 226024 - hypothetical protein VNG0283C False
VNG0315G tfbF CDS 1447201 chromosome 247008 247967 - transcription initiation factor IIB True
VNG0394C CDS 1447254 chromosome 304268 305170 - hypothetical protein VNG0394C False
VNG0424C nac CDS 1447276 chromosome 328415 328807 + nascent polypeptide-associated complex protein True
VNG0467G yafB CDS 1447309 chromosome 359388 360221 - aldehyde reductase False
VNG0491G dnaK CDS 1447329 chromosome 380553 382442 - heat shock protein False
VNG0597H CDS 1447412 chromosome 456082 456483 + hypothetical protein VNG0597H False
VNG0657G coxA2 CDS 1447460 chromosome 501272 503053 - cytochrome c oxidase subunit I False
VNG0666G ctaB CDS 1447466 chromosome 506634 507962 + heme synthase False
VNG0679G acd4 CDS 1447478 chromosome 515836 517029 - acyl-CoA dehydrogenase False
VNG0681G hbd1 CDS 1447480 chromosome 518183 519043 - 3-hydroxyacyl-CoA dehydrogenase False
VNG0703H CDS 1447494 chromosome 531750 532034 + hypothetical protein VNG0703H True
VNG0708H CDS 1447498 chromosome 534840 535388 + hypothetical protein VNG0708H False
VNG0942G cheW2 CDS 1447674 chromosome 719845 720243 - hypothetical protein VNG0942G False
VNG1086C CDS 1447785 chromosome 831651 831929 + hypothetical protein VNG1086C False
VNG1157G rpl7ae CDS 1447838 chromosome 876667 877029 + 50S ribosomal protein L7Ae False
VNG1159G rpl24e CDS 1447840 chromosome 877260 877448 + 50S ribosomal protein L24e False
VNG1253C CDS 1447912 chromosome 944486 945883 - hypothetical protein VNG1253C False
VNG1255C CDS 1447913 chromosome 945880 947262 - replication factor A False
VNG1325C CDS 1447966 chromosome 990944 991744 - hypothetical protein VNG1325C False
VNG1775C CDS 1448300 chromosome 1314713 1315375 - hypothetical protein VNG1775C False
VNG1912G trpD2 CDS 1448404 chromosome 1415175 1416233 + phosphoribosyl transferase False
VNG1914G ppiA CDS 1448405 chromosome 1416274 1416843 + peptidyl-prolyl isomerase False
VNG2133H CDS 1448575 chromosome 1569140 1569532 - hypothetical protein VNG2133H False
VNG2513G aldY1 CDS 1448880 chromosome 1883735 1885204 + AldY1 False
VNG2620G uvrD CDS 1448963 chromosome 1960727 1962556 + hypothetical protein VNG2620G False
VNG7065 sojC CDS 1446795 pNRC100 65313 66251 - chromosome partitioning protein SojC 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.