Organism : Bacillus cereus ATCC14579 | Module List:
Module 407 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 407

There are 10 regulatory influences for Module 407

Regulator Table (10)
Regulator Name Type
BC4425 tf
BC2358 tf
BC3253 tf
BC4053 tf
BC3720 tf
BC3476 tf
BC1673 tf
BC5409 tf
BC5205 tf
BC5402 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
4724 3.80e-02 gaaaaaGaaGGgGAa
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4725 1.60e+03 Ggg.AGCgG
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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 407 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Amino acid transport and metabolism cog subcategory 2.24e-02 3.64e-02 5/33
General function prediction only cog subcategory 2.67e-02 4.27e-02 6/33
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 407

There are 33 genes in Module 407

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0638 BC0638 CDS None chromosome 634970 636433 + Sodium/proton-dependent alanine carrier protein (NCBI ptt file) False
BC0964 BC0964 CDS None chromosome 952361 952906 + Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) False
BC1112 BC1112 CDS None chromosome 1093991 1094968 + Metal-dependent phosphohydrolase (NCBI ptt file) False
BC1142 BC1142 CDS None chromosome 1125310 1125504 - Spore germination protein PD (NCBI ptt file) False
BC1170 BC1170 CDS None chromosome 1149553 1150287 + putative hydrolase (NCBI ptt file) False
BC1407 BC1407 CDS None chromosome 1371024 1371608 + Imidazoleglycerol-phosphate dehydratase (NCBI ptt file) False
BC1413 BC1413 CDS None chromosome 1374406 1375347 + histidinol-phosphatase (RefSeq) False
BC1529 BC1529 CDS None chromosome 1480281 1480922 + DNA polymerase, bacteriophage-type (NCBI ptt file) False
BC1537 BC1537 CDS None chromosome 1486926 1487879 + Biotin operon repressor / Biotin--[acetyl-CoA-carboxylase] synthetase (NCBI ptt file) True
BC1568 BC1568 CDS None chromosome 1514376 1515122 + Methionine aminopeptidase (NCBI ptt file) False
BC2189 BC2189 CDS None chromosome 2135206 2136138 + Aminoglycoside phosphotransferase (NCBI ptt file) False
BC2414 BC2414 CDS None chromosome 2356498 2356638 + Phage protein (NCBI ptt file) False
BC2510 BC2510 CDS None chromosome 2480179 2482419 + Collagen adhesion protein (NCBI ptt file) False
BC2602 BC2602 CDS None chromosome 2566634 2568178 + hypothetical protein (NCBI ptt file) False
BC2777 BC2777 CDS None chromosome 2749636 2750835 - Dihydrolipoamide acetyltransferase component of acetoin dehydrogenase complex (NCBI ptt file) False
BC3164 BC3164 CDS None chromosome 3135303 3135902 - Xanthine dehydrogenase (molybdopterin-guanine dinucleotide biosynthesis subunit) (NCBI ptt file) False
BC3165 BC3165 CDS None chromosome 3135862 3136860 - Xanthine dehydrogenase subunit (NCBI ptt file) False
BC3166 BC3166 CDS None chromosome 3136875 3137324 - Xanthine dehydrogenase iron-sulfur subunit (NCBI ptt file) False
BC3178 BC3178 CDS None chromosome 3149698 3150090 + Lactoylglutathione lyase (NCBI ptt file) False
BC3190 BC3190 CDS None chromosome 3165678 3166550 - Transcriptional regulators, LysR family (NCBI ptt file) True
BC3233 BC3233 CDS None chromosome 3215022 3215171 - Glucose/mannose transporter (NCBI ptt file) False
BC3253 BC3253 CDS None chromosome 3232025 3232852 - Transcriptional regulator, AraC family (NCBI ptt file) True
BC3459 BC3459 CDS None chromosome 3415277 3415555 - hypothetical protein (NCBI ptt file) False
BC3476 BC3476 CDS None chromosome 3429452 3430345 - Transcriptional regulators, LysR family (NCBI ptt file) True
BC3532 BC3532 CDS None chromosome 3500047 3500967 - Glyoxalase family protein (NCBI ptt file) False
BC3638 BC3638 CDS None chromosome 3607379 3608200 - Serine/threonine protein phosphatase (NCBI ptt file) False
BC3646 BC3646 CDS None chromosome 3615642 3617216 - Ferredoxin-dependent glutamate synthase (NCBI ptt file) False
BC3800 BC3800 CDS None chromosome 3775853 3776452 - Dipicolinate synthase, B chain (NCBI ptt file) False
BC3801 BC3801 CDS None chromosome 3776449 3777351 - Dipicolinate synthase, A chain (NCBI ptt file) False
BC3857 BC3857 CDS None chromosome 3835666 3836232 - Thiamin pyrophosphokinase (NCBI ptt file) False
BC4606 BC4606 CDS None chromosome 4555581 4555925 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC4643 BC4643 CDS None chromosome 4583244 4584812 - Metal-dependent hydrolase (NCBI ptt file) False
BC4701 BC4701 CDS None chromosome 4638771 4639316 - 2'-5' RNA ligase (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 407

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.