Organism : Bacillus subtilis | Module List:
Module 313 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 313

There are 20 regulatory influences for Module 313

Regulator Table (20)
Regulator Name Type
BSU23100 tf
BSU09560 tf
BSU37160 tf
BSU12560 tf
BSU24220 tf
BSU33970 tf
BSU24020 tf
BSU32870 tf
BSU25490 tf
BSU05420 tf
BSU37080 tf
BSU29740 tf
BSU19540 tf
BSU05050 tf
BSU25250 tf
BSU19050 tf
BSU09330 tf
BSU35430 tf
BSU28820 tf
BSU07390 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
5564 9.40e-04 AtaGGaGGAaa
Loader icon
5565 6.30e+00 C.gatGGctgccgcg
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 313 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Folding Sorting and Degradation kegg subcategory 2.52e-04 1.95e-03 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein fate tigr mainrole 1.06e-03 1.73e-03 3/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 3.18e-03 5.41e-03 11/30
General function prediction only cog subcategory 1.44e-03 2.56e-03 8/30
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 313

There are 30 genes in Module 313

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU02700 estA CDS None chromosome 291757 292395 + secreted alkaliphilic lipase (RefSeq) False
BSU04010 sipU CDS None chromosome 453584 454147 + type I signal peptidase (RefSeq) False
BSU06190 ydjG CDS None chromosome 671542 672567 + putative phage replication protein (RefSeq) False
BSU06200 ydjH CDS None chromosome 672567 673331 + hypothetical protein (RefSeq) False
BSU09890 natA CDS None chromosome 1061899 1062795 + Na+-efflux ABC transporter (ATP-binding protein) (RefSeq) False
BSU09900 natB CDS None chromosome 1062788 1064047 + Na+ exporter (ABC permease) (RefSeq) False
BSU10760 yisL CDS None chromosome 1152570 1152926 + hypothetical protein (RefSeq) False
BSU11170 yitY CDS None chromosome 1192162 1193592 + putative FMN/FAD-binding oxidoreductase (RefSeq) False
BSU11180 yitZ CDS None chromosome 1193637 1194131 + putative transport protein (RefSeq) False
BSU14110 ykuK CDS None chromosome 1483772 1484290 + putative RNAse (RefSeq) False
BSU14180 dapH CDS None chromosome 1488280 1488990 + tetrahydrodipicolinate N-acetyltransferase (RefSeq) False
BSU14190 dapL CDS None chromosome 1489060 1490184 + N-acetyl-diaminopimelate deacetylase (RefSeq) False
BSU14350 yknX CDS None chromosome 1503589 1504722 + putative efflux permease (RefSeq) False
BSU14530 rnjA CDS None chromosome 1522425 1524092 - ribonuclease J1 (RefSeq) False
BSU15010 ylbH CDS None chromosome 1568825 1569319 + putative enzyme with adenosyl binding site (RefSeq) False
BSU15020 coaD CDS None chromosome 1569383 1569868 + phosphopantetheine adenylyltransferase (RefSeq) False
BSU16080 ylqH CDS None chromosome 1679277 1679558 + putative flagellar biosynthesis protein (RefSeq) False
BSU16950 pbpX CDS None chromosome 1765128 1766303 + penicillin-binding endopeptidase X (RefSeq) False
BSU19630 deoD CDS None chromosome 2134669 2135370 - purine nucleoside phosphorylase (RefSeq) False
BSU27900 pheA CDS None chromosome 2850509 2851366 - prephenate dehydratase (RefSeq) False
BSU29930 amyX CDS None chromosome 3060700 3062856 - pullulanase (RefSeq) False
BSU29940 ytlR CDS None chromosome 3062882 3063811 - putative phospholipid kinase (RefSeq) False
BSU33880 yvbJ CDS None chromosome 3473137 3474954 - hypothetical protein (RefSeq) False
BSU34020 yvbX CDS None chromosome 3490686 3491720 - putative epimerase modification of peptidoglycan (RefSeq) False
BSU39600 yxeC CDS None chromosome 4065622 4066020 - putative integral inner membrane protein (RefSeq) False
BSU40600 yybL CDS None chromosome 4173434 4174144 + putative integral inner membrane protein (RefSeq) False
BSU40610 yybK CDS None chromosome 4174141 4174896 + putative integral inner membrane protein (RefSeq) False
BSU40620 yybJ CDS None chromosome 4174893 4175549 + putative ATP-binding cassette protein (RefSeq) False
BSU41030 jag CDS None chromosome 4212224 4212850 - SpoIIIJ-associated RNA/ssDNA-binding protein (RefSeq) False
BSU41040 spoIIIJ CDS None chromosome 4212847 4213632 - OxaA-like protein precursor (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 313

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.