Organism : Bacillus subtilis | Module List:
Module 239 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 239

There are 19 regulatory influences for Module 239

Regulator Table (19)
Regulator Name Type
BSU18760 tf
BSU14380 tf
BSU26580 tf
BSU19120 tf
BSU04730 tf
BSU12560 tf
BSU19100 tf
BSU00800 tf
BSU19090 tf
BSU29700 tf
BSU04680 tf
BSU14240 tf
BSU10420 tf
BSU35650 tf
BSU01740 tf
BSU37620 tf
BSU33970 tf
BSU34220 tf
BSU11500 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
5420 6.50e-02 aataaGgaGGAagaAa
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5421 2.70e-01 aCAGccg.taTTaTGaat.cA
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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 239 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes tigr mainrole 1.35e-03 2.14e-03 4/29
Sporulation and germination tigr sub1role 1.87e-04 3.58e-04 4/29

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 239

There are 29 genes in Module 239

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU05380 ydfE CDS None chromosome 584699 585322 - putative flavoprotein (RefSeq) False
BSU12460 xlyB CDS None chromosome 1316849 1317802 + N-acetylmuramoyl-L-alanine amidase; bacteriophage PBSX protein (RefSeq) False
BSU12680 xkdO CDS None chromosome 1334279 1338277 + conserved hypothetical protein; PBSX phage protein (RefSeq) False
BSU12710 xkdR CDS None chromosome 1339922 1340188 + conserved hypothetical protein; putative PBSX prophage protein (RefSeq) False
BSU12790 xhlA CDS None chromosome 1346043 1346312 + defective prophage PBSX putative enzyme (RefSeq) False
BSU13480 ykrK CDS None chromosome 1413433 1414134 - hypothetical protein (RefSeq) False
BSU14750 ylaE CDS None chromosome 1544243 1544854 - hypothetical protein (RefSeq) False
BSU14800 ylaJ CDS None chromosome 1547988 1548617 - putative lipoprotein (RefSeq) False
BSU18600 yozQ CDS None chromosome 2028231 2028524 + hypothetical protein (RefSeq) False
BSU18760 yoaU CDS None chromosome 2044166 2045038 - putative transcriptional regulator (LysR family) (RefSeq) True
BSU18920 phrK CDS None chromosome 2062473 2062595 + secreted regulator of the activity of phosphatase RapK (RefSeq) False
BSU19090 yobU CDS None chromosome 2081742 2082224 - putative effector of transcriptional regulator (RefSeq) True
BSU19400 sodC CDS None chromosome 2113944 2114534 - superoxide dismutase (exported lipoprotein) (RefSeq) False
BSU19410 cwlS CDS None chromosome 2114627 2115871 - peptidoglycan hydrolase (cell wall-binding d,l-endopeptidase) (RefSeq) False
BSU22000 sspL CDS None chromosome 2310056 2310184 + small acid-soluble spore protein (RefSeq) False
BSU24590 yqhG CDS None chromosome 2550701 2551495 + hypothetical protein (RefSeq) False
BSU25060 yqfZ CDS None chromosome 2587934 2588233 + factor involved in motility (RefSeq) False
BSU25120 yqfT CDS None chromosome 2592233 2592487 + hypothetical protein (RefSeq) False
BSU26120 yqbG CDS None chromosome 2681712 2682107 - conserved hypothetical protein; skin element (RefSeq) False
BSU26940 yraH CDS None chromosome 2751392 2751778 - putative lyase (RefSeq) False
BSU27570 yrzK CDS None chromosome 2817417 2817587 - hypothetical protein (RefSeq) False
BSU27670 spoVB CDS None chromosome 2828790 2830346 + putative putative translocase with flippase function for teichoic acid synthesis; involved in spore cortex synthesis (stage V sporulation) (RefSeq) False
BSU29910 ytzH CDS None chromosome 3059444 3059722 + hypothetical protein (RefSeq) False
BSU32270 yutH CDS None chromosome 3315356 3316375 - spore coat-associated protein (RefSeq) False
BSU32280 yutG CDS None chromosome 3316528 3317028 + putative phosphatidylglycerophosphatase A (RefSeq) False
BSU32320 yutC CDS None chromosome 3318702 3319334 + putative lipoprotein (RefSeq) False
BSU35770 tagC CDS None chromosome 3682468 3683796 + putative polyglycerol phosphate assembly and export protein (teichoic acid biosynthesis) (RefSeq) False
BSU36090 ywrE CDS None chromosome 3717821 3718156 + hypothetical protein (RefSeq) False
BSU38800 yxkH CDS None chromosome 3982206 3983045 - putative exported polysaccharide deacetylase, lipoprotein (RefSeq) 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 239

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.