Organism : Bacillus cereus ATCC14579 | Module List:
Module 139 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 139

There are 9 regulatory influences for Module 139

Regulator Table (9)
Regulator Name Type
BC3084 tf
BC1302 tf
BC3792 tf
BC4652 tf
BC2386 tf
BC4010 tf
BC5481 tf
BC4703 tf
BC0099 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
4194 1.60e-04 gAgGgGga
Loader icon
4195 1.30e+04 GGGTGGTAaCaCGG
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 139 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 5.71e-04 9.95e-04 4/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell wall/membrane/envelope biogenesis cog subcategory 1.82e-02 3.01e-02 3/32
General function prediction only cog subcategory 2.27e-02 3.69e-02 6/32
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 139

There are 32 genes in Module 139

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0041 BC0041 CDS None chromosome 39715 40590 + Corrin/porphyrin methyltransferase (NCBI ptt file) False
BC0374 BC0374 CDS None chromosome 355507 356622 + Amidohydrolase amhX (NCBI ptt file) False
BC0494 BC0494 CDS None chromosome 485536 485655 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC0820 BC0820 CDS None chromosome 804545 805861 - Branched-chain amino acid transport system carrier protein (NCBI ptt file) False
BC0859 BC0859 CDS None chromosome 833052 834791 - Oligopeptide-binding protein oppA (NCBI ptt file) False
BC1230 BC1230 CDS None chromosome 1204867 1205265 - Bacterial Ig-like domain protein (NCBI ptt file) False
BC1231 BC1231 CDS None chromosome 1205421 1206899 - Sodium/proline symporter (NCBI ptt file) False
BC1441 BC1441 CDS None chromosome 1400633 1402024 - Branched-chain amino acid transport system carrier protein (NCBI ptt file) False
BC1817 BC1817 CDS None chromosome 1774467 1775117 - CAAX amino terminal protease family (NCBI ptt file) False
BC1985 BC1985 DUMMY None chromosome 0 0 + None False
BC2094 BC2094 CDS None chromosome 2038877 2039662 - Acetyltransferase (NCBI ptt file) False
BC2160 BC2160 CDS None chromosome 2103260 2103589 + hypothetical protein (NCBI ptt file) False
BC2464 BC2464 CDS None chromosome 2428176 2429627 + S-layer protein / Peptidoglycan endo-beta-N-acetylglucosaminidase (NCBI ptt file) False
BC2496 BC2496 CDS None chromosome 2465720 2466736 - D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) False
BC2699 BC2699 DUMMY None chromosome 0 0 + None False
BC2715 BC2715 CDS None chromosome 2692233 2692808 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC3075 BC3075 CDS None chromosome 3030703 3031335 - EpiH/GdmH-related protein (NCBI ptt file) False
BC3117 BC3117 CDS None chromosome 3084561 3085712 + Arsenical pump membrane protein (NCBI ptt file) False
BC3524 BC3524 CDS None chromosome 3485501 3486733 - S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) False
BC3788 BC3788 CDS None chromosome 3760355 3761314 - Nucleoside transport system permease protein (NCBI ptt file) False
BC3789 BC3789 DUMMY None chromosome 0 0 + None False
BC3893 lspA CDS None chromosome 3874378 3874836 - lipoprotein signal peptidase (RefSeq) False
BC4010 BC4010 CDS None chromosome 3984679 3985701 - Transcriptional regulator, LacI family (NCBI ptt file) True
BC4121 BC4121 CDS None chromosome 4084181 4085554 + Tyrosine transporter (NCBI ptt file) False
BC4122 BC4122 DUMMY None chromosome 0 0 + None False
BC4449 BC4449 CDS None chromosome 4388199 4391474 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC4852 BC4852 CDS None chromosome 4776349 4776573 + hypothetical protein (NCBI ptt file) False
BC5051 BC5051 CDS None chromosome 4954735 4956177 - Sodium/proton-dependent alanine carrier protein (NCBI ptt file) False
BC5062 BC5062 CDS None chromosome 4969365 4970627 - Tyrosyl-tRNA synthetase (NCBI ptt file) False
BC5302 BC5302 CDS None chromosome 5211310 5214039 + Sensory box/GGDEF family protein (NCBI ptt file) False
BC5350 BC5350 CDS None chromosome 5260317 5261174 - Transcriptional activator plcR (NCBI ptt file) False
BC5366 BC5366 CDS None chromosome 5284155 5285141 + Muramoyltetrapeptide carboxypeptidase (NCBI ptt file) 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 139

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.