Organism : Bacillus cereus ATCC14579 | Module List:
Module 425 Profile

GeneModule member RegulatorRegulator MotifMotif
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 425

There are 15 regulatory influences for Module 425

Regulator Table (15)
Regulator Name Type
BC0123 tf
BC3891 tf
BC5059 tf
BC3814 tf
BC4256 tf
BC0607 tf
BC0613 tf
BC4652 tf
BC1756 tf
BC4222 tf
BC0648 tf
BC4703 tf
BC0122 tf
BC0114 tf
BC4670 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
4760 1.40e+00 ccc.Gt.aggttGagaagg
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4761 2.20e+01 GAGAggag
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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 425 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.60e-05 3.06e-04 11/21
Nucleotide Metabolism kegg subcategory 0.00e+00 0.00e+00 8/21
Pyrimidine metabolism kegg pathway 0.00e+00 0.00e+00 8/21
Amino Acid Metabolism kegg subcategory 2.42e-02 4.57e-02 3/21
Alanine aspartate and glutamate metabolism kegg pathway 7.00e-06 1.60e-04 3/21
Glycan Biosynthesis and Metabolism kegg subcategory 2.00e-06 5.40e-05 3/21
Peptidoglycan biosynthesis kegg pathway 2.00e-06 5.40e-05 3/21
Global kegg category 3.00e-06 7.90e-05 11/21
Metabolism kegg subcategory 3.00e-06 7.90e-05 11/21
Metabolic pathways kegg pathway 1.00e-06 3.00e-05 11/21

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 0.00e+00 0.00e+00 6/21
Pyrimidine ribonucleotide biosynthesis tigr sub1role 0.00e+00 0.00e+00 6/21
Cell envelope tigr mainrole 5.20e-05 1.17e-04 3/21
Biosynthesis and degradation of murein sacculus and peptidoglycan tigr sub1role 5.00e-06 1.50e-05 3/21

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.63e-03 3.14e-03 7/21
Metabolism cog category 3.66e-04 7.97e-04 12/21
Cell wall/membrane/envelope biogenesis cog subcategory 2.00e-06 1.20e-05 6/21
Nucleotide transport and metabolism cog subcategory 0.00e+00 0.00e+00 9/21
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 425

There are 21 genes in Module 425

Gene Member Table (21)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0061 BC0061 CDS None chromosome 60333 61793 + MazG protein (NCBI ptt file) False
BC0865 BC0865 CDS None chromosome 840791 842215 - Arginine/ornithine antiporter (NCBI ptt file) False
BC0902 BC0902 CDS None chromosome 889994 891586 + S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) False
BC0919 BC0919 CDS None chromosome 906781 907059 + hypothetical protein (NCBI ptt file) False
BC3882 BC3882 CDS None chromosome 3861625 3862257 - Orotate phosphoribosyltransferase (NCBI ptt file) False
BC3883 BC3883 CDS None chromosome 3862254 3862970 - Orotidine 5'-phosphate decarboxylase (NCBI ptt file) False
BC3884 BC3884 CDS None chromosome 3862955 3863884 - Dihydroorotate dehydrogenase, catalytic subunit (NCBI ptt file) False
BC3885 BC3885 CDS None chromosome 3863881 3864660 - Dihydroorotate dehydrogenase electron transfer subunit (NCBI ptt file) False
BC3886 BC3886 CDS None chromosome 3864657 3867875 - Carbamoyl-phosphate synthase large chain (NCBI ptt file) False
BC3887 BC3887 CDS None chromosome 3867860 3868981 - Carbamoyl-phosphate synthase small chain (NCBI ptt file) False
BC3888 BC3888 CDS None chromosome 3868954 3870240 - Dihydroorotase (NCBI ptt file) False
BC3889 BC3889 CDS None chromosome 3870224 3871129 - Aspartate carbamoyltransferase (NCBI ptt file) False
BC3890 BC3890 CDS None chromosome 3871287 3872633 - Uracil permease (NCBI ptt file) False
BC3891 BC3891 CDS None chromosome 3872719 3873261 - Uracil phosphoribosyltransferase (NCBI ptt file) True
BC3908 BC3908 CDS None chromosome 3888507 3889277 - Cell division protein ftsQ (NCBI ptt file) False
BC3909 BC3909 CDS None chromosome 3889376 3890281 - UDP-N-acetylenolpyruvoylglucosamine reductase (NCBI ptt file) False
BC3910 BC3910 CDS None chromosome 3890494 3891588 - UDP-N-acetylglucosamine--N-acetylmuramyl-(Pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase (NCBI ptt file) False
BC3913 BC3913 CDS None chromosome 3894227 3895201 - Phospho-N-acetylmuramoyl-pentapeptide-transferase (NCBI ptt file) False
BC3915 BC3915 CDS None chromosome 3896885 3898801 - Stage V sporulation protein D / Sporulation specific D,D-transpeptidase (NCBI ptt file) False
BC5435 BC5435 CDS None chromosome 5355630 5358746 + Acriflavin resistance plasma membrane protein (NCBI ptt file) False
BC5442 BC5442 CDS None chromosome 5365293 5366591 + Transporter, MFS superfamily (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.

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.