Organism : Halobacterium salinarum NRC-1 | Module List:
Module 77 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 77

There are 7 regulatory influences for Module 77

Regulator Table (7)
Regulator Name Type
VNG1483C tf
VNG2441G
VNG0751C
combiner
VNG5028G
VNG1899G
combiner
VNG1899G
VNG2094G
combiner
VNG0458G
VNG2476C
combiner
VNG0458G
VNG1922G
combiner
VNG1899G
VNG0536G
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
1129 3.60e-01 TG.gA.cAaacCCcaTaaTaaTaT
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1130 7.40e+02 AcAccccacAc
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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 77 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 12/33
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 12/33
Environmental Information Processing kegg category 0.00e+00 0.00e+00 14/33
Metabolism of Cofactors and Vitamins kegg subcategory 2.19e-02 4.36e-02 3/33
Environmental Information Processing kegg category 0.00e+00 0.00e+00 13/33
Membrane Transport kegg subcategory 0.00e+00 0.00e+00 12/33
ABC transporters kegg pathway 0.00e+00 0.00e+00 12/33

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
transport biological_process 5.00e-06 3.10e-05 6/33
phosphate ion transport biological_process 8.00e-06 4.80e-05 3/33
transporter activity molecular_function 1.00e-06 5.00e-06 6/33
inorganic phosphate transmembrane transporter activity molecular_function 8.00e-06 3.60e-05 3/33
ATP binding molecular_function 3.21e-02 3.93e-02 5/33
oxidoreductase activity molecular_function 8.75e-03 1.24e-02 3/33
ATPase activity molecular_function 1.25e-03 2.40e-03 3/33

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Anions tigr sub1role 8.00e-06 5.20e-05 3/33
Transport and binding proteins tigr mainrole 6.00e-06 1.01e-04 5/33
Amino acid biosynthesis tigr mainrole 5.00e-04 3.14e-03 3/33
Transport and binding proteins tigr mainrole 6.00e-06 1.30e-05 5/33
Anions tigr sub1role 8.00e-06 1.90e-05 3/33
Amino acid biosynthesis tigr mainrole 5.00e-04 8.43e-04 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Signal transduction mechanisms cog subcategory 1.57e-03 1.65e-02 4/33
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 13/33
Inorganic ion transport and metabolism cog subcategory 0.00e+00 0.00e+00 11/33
Metabolism cog category 0.00e+00 0.00e+00 26/33
Metabolism cog category 3.00e-06 9.00e-06 20/33
Signal transduction mechanisms cog subcategory 1.57e-03 2.84e-03 4/33
Amino acid transport and metabolism cog subcategory 0.00e+00 0.00e+00 13/33
Inorganic ion transport and metabolism cog subcategory 0.00e+00 0.00e+00 11/33
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 77

There are 33 genes in Module 77

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
VNG0745G spoVR CDS 1447527 chromosome 560272 562254 - hypothetical protein VNG0745G False
VNG0746C CDS 1447528 chromosome 562241 563569 - hypothetical protein VNG0746C False
VNG0748G prkA CDS 1447529 chromosome 563560 565773 - hypothetical protein VNG0748G False
VNG0749G prk CDS 1447530 chromosome 565827 567884 - serine protein kinase False
VNG0750C CDS 1447531 chromosome 568228 568947 + hypothetical protein VNG0750C False
VNG1018G adh3 CDS 1447734 chromosome 780246 782048 + alcohol dehydrogenase False
VNG1021C CDS 1447736 chromosome 782934 783695 + GTP cyclohydrolase III False
VNG1023C CDS 1447737 chromosome 783700 784716 + hypothetical protein VNG1023C False
VNG1024C CDS 1447738 chromosome 784713 785120 + hypothetical protein VNG1024C False
VNG1025H CDS 1447739 chromosome 785117 785962 + hypothetical protein VNG1025H False
VNG1295H CDS 1447941 chromosome 967595 967786 - hypothetical protein VNG1295H False
VNG1760G htr5 CDS 1448288 chromosome 1298933 1301365 - Htr5 False
VNG1821G adh4 CDS 1448333 chromosome 1345983 1347026 - alcohol dehydrogenase False
VNG1925H CDS 1448415 chromosome 1421025 1421192 + hypothetical protein VNG1925H 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
VNG2363Gm oppD1 CDS 1449067 chromosome 1769595 1770602 + oligopeptide ABC transporter ATP-binding protein False
VNG2365G appF CDS 1448762 chromosome 1770599 1771921 + oligopeptide ABC transporter ATP-binding protein False
VNG2430G thrC1 CDS 1448815 chromosome 1825082 1826329 - threonine synthase False
VNG2436G argH CDS 1448819 chromosome 1827624 1829081 - argininosuccinate lyase False
VNG2437G argG CDS 1448820 chromosome 1829078 1830268 - argininosuccinate synthase False
VNG2477H CDS 1448851 chromosome 1855271 1855378 - hypothetical protein VNG2477H 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
VNG2527G dppD CDS 1448893 chromosome 1895306 1897006 + hypothetical protein VNG2527G 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
VNG2616G cxp CDS 1448960 chromosome 1957549 1959057 + putative carboxypeptidase False
VNG6301G aph CDS 1449184 pNRC200 232702 234123 - alkaline phosphatase 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 77

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

comments powered by Disqus
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.