Organism : Bacillus subtilis | Module List:
Module 115 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 115

There are 10 regulatory influences for Module 115

Regulator Table (10)
Regulator Name Type
BSU05240 tf
BSU03880 tf
BSU05060 tf
BSU05460 tf
BSU00560 tf
BSU11930 tf
BSU09430 tf
BSU05180 tf
BSU05850 tf
BSU05150 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
5184 1.50e+00 TtATGaaCAGCa.GcTTcaaTAAA
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5185 5.90e-02 ctaTttaa.AtaAaGtgAatg
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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 115 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 2.68e-02 4.08e-02 10/34
Transcription cog subcategory 7.00e-03 1.15e-02 6/34
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 115

There are 34 genes in Module 115

Gene Member Table (34)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BSU00440 veg CDS None chromosome 52761 53021 + hypothetical protein (RefSeq) False
BSU01800 alkA CDS None chromosome 202533 203444 - DNA-3-methyladenine glycosylase (RefSeq) False
BSU03140 tmrB CDS None chromosome 338716 339309 - ATP-binding tunicamycin resistance protein (RefSeq) False
BSU03150 aroK CDS None chromosome 339585 340145 + shikimate kinase (RefSeq) False
BSU03540 ycxB CDS None chromosome 404030 404587 - hypothetical protein (RefSeq) False
BSU03880 yczG CDS None chromosome 439277 439591 + putative transcriptional regulator (ArsR family) (RefSeq) True
BSU04610 ydcA CDS None chromosome 514577 515176 - hypothetical protein (RefSeq) False
BSU05060 lrpB CDS None chromosome 551595 552044 - transcriptional regulator (Lrp/AsnC family) (RefSeq) True
BSU05090 yddS CDS None chromosome 554212 555522 + putative permease (RefSeq) False
BSU05110 ydeA CDS None chromosome 557952 558545 + putative enzyme (RefSeq) False
BSU05170 ydeE CDS None chromosome 563158 564030 - putative transcriptional regulator (AraC/XylS family) (RefSeq) True
BSU05180 ydeF CDS None chromosome 564248 565645 + putative PLP-dependent transcriptional regulator (RefSeq) True
BSU05200 ydeH CDS None chromosome 567206 567652 + putative integral inner membrane protein (RefSeq) False
BSU05210 ydeI CDS None chromosome 567889 568482 + hypothetical protein (RefSeq) False
BSU05240 ydeL CDS None chromosome 570933 572324 + putative PLP-dependent transcriptional regulator (RefSeq) True
BSU05460 ydfL CDS None chromosome 593730 594542 - putative transcriptional regulator of efflux transporter (RefSeq) True
BSU08360 yfiQ CDS None chromosome 910175 911263 + putative membrane component involved in biofilm formation (RefSeq) False
BSU09600 crcBA CDS None chromosome 1036261 1036617 - camphor resistance protein CrcB (RefSeq) False
BSU09760 yheE CDS None chromosome 1049751 1049969 - hypothetical protein (RefSeq) False
BSU11510 yjbE CDS None chromosome 1227448 1228104 - putative transporter component (RefSeq) False
BSU12200 yjiA CDS None chromosome 1289985 1290263 - hypothetical protein (RefSeq) False
BSU13370 ykoQ CDS None chromosome 1400075 1400887 - putative metallophosphoesterase (RefSeq) False
BSU17060 ymzD CDS None chromosome 1779888 1780343 - putative integral inner membrane protein (RefSeq) False
BSU18790 yoaZ CDS None chromosome 2046885 2047517 - putative factor of the oxidative stress response (RefSeq) False
BSU26580 bltR CDS None chromosome 2715261 2716082 - transcriptional regulator (RefSeq) True
BSU26590 blt CDS None chromosome 2716199 2717401 + efflux transporter (RefSeq) False
BSU26600 bltD CDS None chromosome 2717570 2718028 + spermine/spermidine acetyltransferase (RefSeq) False
BSU30680 ytjA CDS None chromosome 3137145 3137372 + hypothetical protein (RefSeq) False
BSU32190 yuzB CDS None chromosome 3307393 3307629 - hypothetical protein (RefSeq) False
BSU33130 liaI CDS None chromosome 3397576 3397956 - permease (RefSeq) False
BSU37540 ywhB CDS None chromosome 3852508 3852696 + 4-oxalocrotonate tautomerase (RefSeq) False
BSU40140 yydJ CDS None chromosome 4123244 4123966 - putative permease for export of a regulatory peptide (RefSeq) False
BSU40150 yydI CDS None chromosome 4123987 4124616 - ABC transporter (ATP-binding protein) (RefSeq) False
BSU40980 yyaB CDS None chromosome 4206430 4206870 + putative integral inner membrane protein (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 115

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.