Organism : Halobacterium salinarum NRC-1 | Module List:
Module 12 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 12

There are 4 regulatory influences for Module 12

Regulator Table (4)
Regulator Name Type
VNG1496G
VNG0320H		 combiner
VNG0040C
VNG0293H		 combiner
VNG1029C
VNG2641H		 combiner
VNG0293H
VNG0703H		 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
1003 8.00e-06 g.AAatctttaAgT
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1004 1.00e-01 agaaAt.gg.TgT.cgtAT
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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 12 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 1.94e-04 1.26e-03 3/30
Carbon fixation pathways in prokaryotes kegg pathway 3.43e-04 1.78e-03 3/30
Microbial metabolism in diverse environments kegg pathway 2.68e-02 3.97e-02 3/30
Energy Metabolism kegg subcategory 4.82e-04 2.82e-03 6/30
Carbohydrate Metabolism kegg subcategory 1.84e-02 3.90e-02 3/30
Citrate cycle (TCA cycle) kegg pathway 1.94e-04 1.47e-03 3/30
Energy Metabolism kegg subcategory 9.84e-04 4.78e-03 5/30
Carbon fixation pathways in prokaryotes kegg pathway 3.43e-04 2.17e-03 3/30

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
regulation of transcription, DNA-dependent biological_process 1.42e-02 1.88e-02 3/30
cellular component movement biological_process 2.00e-06 1.00e-05 3/30
DNA binding molecular_function 2.57e-02 3.21e-02 3/30
structural molecule activity molecular_function 1.50e-05 5.90e-05 3/30
protein binding molecular_function 2.87e-04 6.89e-04 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein fate tigr mainrole 1.57e-04 1.63e-03 3/30
Protein fate tigr mainrole 1.57e-04 3.09e-04 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Archaeal flagellins cog 1.00e-06 1.00e-06 3/30
Cell motility cog subcategory 1.42e-03 1.62e-02 3/30
Posttranslational modification, protein turnover, chaperones cog subcategory 2.80e-04 4.99e-03 5/30
Energy production and conversion cog subcategory 6.20e-04 8.83e-03 6/30
Cellular processes and signaling cog category 4.92e-04 8.09e-03 10/30
Cellular processes and signaling cog category 1.58e-04 3.75e-04 10/30
Transcription cog subcategory 2.92e-02 4.36e-02 3/30
Cell motility cog subcategory 1.42e-03 2.60e-03 3/30
Posttranslational modification, protein turnover, chaperones cog subcategory 2.80e-04 5.76e-04 5/30
Energy production and conversion cog subcategory 6.20e-04 1.22e-03 6/30
Archaeal flagellins cog 1.00e-06 2.00e-06 3/30
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 12

There are 30 genes in Module 12

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0162G alkK CDS 1447089 chromosome 136676 138478 + AlkK False
VNG0192G ftsZ2 CDS 1447112 chromosome 165152 166279 - cell division protein FtsZ False
VNG0194H CDS 1447113 chromosome 166336 166503 - hypothetical protein VNG0194H True
VNG0207H CDS 1447124 chromosome 175115 175471 + hypothetical protein VNG0207H False
VNG0208H CDS 1447125 chromosome 175471 175920 + hypothetical protein VNG0208H False
VNG0209H CDS 1447126 chromosome 175913 176947 + hypothetical protein VNG0209H False
VNG0254G tfbG CDS 1447159 chromosome 208286 209257 - transcription initiation factor IIB True
VNG0258H CDS 1447162 chromosome 210639 210989 - hypothetical protein VNG0258H True
VNG0259G ipp CDS 1447163 chromosome 211101 211634 + inorganic pyrophosphatase False
VNG0261H CDS 1447164 chromosome 211694 211852 + hypothetical protein VNG0261H False
VNG0262C CDS 1447165 chromosome 211896 213011 + hypothetical protein VNG0262C False
VNG0524G yurY CDS 1447354 chromosome 404888 405814 + ABC transporter ATP-binding protein False
VNG0525C CDS 1447355 chromosome 405851 407275 + hypothetical protein VNG0525C False
VNG0527C CDS 1447356 chromosome 407277 408491 + hypothetical protein VNG0527C False
VNG0801C CDS 1447571 chromosome 603037 603327 - hypothetical protein VNG0801C False
VNG0880G psmA CDS 1447627 chromosome 664212 664979 + proteasome subunit alpha False
VNG0960G flaB1 CDS 1447685 chromosome 731799 732380 + flagellin B1 False
VNG0961G flaB2 CDS 1447686 chromosome 732464 732982 + flagellin B2 False
VNG0962G flaB3 CDS 1447687 chromosome 733066 733575 + flagellin B3 False
VNG0963G cpcE CDS 1447688 chromosome 733804 734865 + phycocyanin alpha phycocyanobilin lyase-like protein False
VNG0964C CDS 1447689 chromosome 735009 735881 + hypothetical protein VNG0964C False
VNG1125G korB CDS 1447814 chromosome 855719 856657 - KorB False
VNG1128G korA CDS 1447815 chromosome 856660 858582 - KorA False
VNG1306G sdhA CDS 1447950 chromosome 976559 978406 - hypothetical protein VNG1306G False
VNG1412H CDS 1448029 chromosome 1051252 1052118 - hypothetical protein VNG1412H False
VNG1836G cspD2 CDS 1448345 chromosome 1356243 1356452 + cold shock protein True
VNG2226G cctA CDS 1448653 chromosome 1656061 1657806 - thermosome subunit alpha False
VNG2443G dpsA CDS 1448825 chromosome 1833843 1834391 - starvation induced DNA-binding protein False
VNG2543C CDS 1448903 chromosome 1906294 1906926 - hypothetical protein VNG2543C False
VNG6313G nhaC3 CDS 1449193 pNRC200 242960 244417 - Na+/H+ antiporter 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.