Organism : Bacillus cereus ATCC14579 | Module List:
Module 351 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 351

There are 18 regulatory influences for Module 351

Regulator Table (18)
Regulator Name Type
BC4336 tf
BC5340 tf
BC5222 tf
BC1047 tf
BC0047 tf
BC0958 tf
BC3588 tf
BC3593 tf
BC2401 tf
BC3255 tf
BC3497 tf
BC5097 tf
BC2181 tf
BC4968 tf
BC0801 tf
BC3903 tf
BC2514 tf
BC1715 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
4612 8.30e-08 gaGaaGGag
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4613 1.70e+03 aaAAaGAg.gG
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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 351 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Genetic Information Processing kegg category 1.62e-02 3.42e-02 4/37
Replication and Repair kegg subcategory 2.20e-05 3.86e-04 4/37
Nucleotide excision repair kegg pathway 0.00e+00 0.00e+00 4/37

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 7.00e-06 2.30e-05 5/37
DNA replication, recombination, and repair tigr sub1role 4.00e-06 1.30e-05 5/37

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 4.10e-05 1.23e-04 6/37
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 351

There are 37 genes in Module 351

Gene Member Table (37)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0034 BC0034 CDS None chromosome 34129 34308 + CsfB protein (NCBI ptt file) False
BC0286 BC0286 CDS None chromosome 250304 250777 + ATP/GTP hydrolase (NCBI ptt file) False
BC0287 BC0287 CDS None chromosome 250758 251450 + Glycoprotease protein family (NCBI ptt file) False
BC0288 BC0288 CDS None chromosome 251485 251907 + Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) False
BC0341 BC0341 CDS None chromosome 317208 319217 + NAD-dependent DNA ligase (NCBI ptt file) False
BC0391 BC0391 CDS None chromosome 369985 370653 + hypothetical protein (NCBI ptt file) False
BC0392 BC0392 CDS None chromosome 370892 372157 + hypothetical protein (NCBI ptt file) False
BC0818 BC0818 CDS None chromosome 802658 803497 + Oligopeptide transport system permease protein oppB (NCBI ptt file) False
BC0942 BC0942 CDS None chromosome 926514 927269 + hypothetical protein (NCBI ptt file) False
BC1141 BC1141 CDS None chromosome 1124908 1125282 - Spore germination protein PE (NCBI ptt file) False
BC1142 BC1142 CDS None chromosome 1125310 1125504 - Spore germination protein PD (NCBI ptt file) False
BC1143 BC1143 CDS None chromosome 1125511 1126125 - Spore germination protein PC (NCBI ptt file) False
BC1494 BC1494 CDS None chromosome 1449547 1450005 + N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) False
BC1550 BC1550 CDS None chromosome 1498071 1499759 - Multimodular transpeptidase-transglycosylase PBP 1A (NCBI ptt file) False
BC1559 BC1559 CDS None chromosome 1505785 1506351 + Spore coat protein (NCBI ptt file) False
BC2377 BC2377 CDS None chromosome 2321386 2322174 - hypothetical protein (NCBI ptt file) False
BC2416 BC2416 CDS None chromosome 2358812 2359621 - hypothetical protein (NCBI ptt file) False
BC2541 BC2541 CDS None chromosome 2514266 2515894 + ABC transporter ATP-binding protein (NCBI ptt file) False
BC2542 BC2542 CDS None chromosome 2515915 2516499 + Acetyltransferase (NCBI ptt file) False
BC2544 BC2544 CDS None chromosome 2517503 2519437 + ABC transporter permease protein (NCBI ptt file) False
BC3087 BC3087 CDS None chromosome 3042244 3044850 - Phosphoenolpyruvate synthase (NCBI ptt file) False
BC3255 BC3255 CDS None chromosome 3235900 3239313 - Molybdate metabolism regulator (NCBI ptt file) True
BC3474 BC3474 CDS None chromosome 3428154 3428630 - hypothetical protein (NCBI ptt file) False
BC3593 BC3593 CDS None chromosome 3569404 3570372 - Transcriptional regulator, DeoR family (NCBI ptt file) True
BC4399 BC4399 CDS None chromosome 4339553 4339729 - hypothetical protein (NCBI ptt file) False
BC4520 uvrC CDS None chromosome 4464276 4466060 - excinuclease ABC subunit C (RefSeq) False
BC4577 BC4577 CDS None chromosome 4522561 4523328 - hypothetical protein (NCBI ptt file) False
BC4579 BC4579 CDS None chromosome 4523907 4524845 - Primosomal protein dnaI (NCBI ptt file) False
BC5166 BC5166 CDS None chromosome 5063161 5063610 - hypothetical protein (NCBI ptt file) False
BC5167 BC5167 CDS None chromosome 5063670 5066546 - Excinuclease ABC subunit A (NCBI ptt file) False
BC5168 BC5168 CDS None chromosome 5066552 5068528 - Excinuclease ABC subunit B (NCBI ptt file) False
BC5204 BC5204 CDS None chromosome 5104382 5105119 + Peptidoglycan N-acetylglucosamine deacetylase (NCBI ptt file) False
BC5221 BC5221 CDS None chromosome 5121328 5123328 - Phage infection protein (NCBI ptt file) False
BC5223 BC5223 CDS None chromosome 5124396 5125490 - hypothetical Exported Protein (NCBI ptt file) False
BC5347 BC5347 CDS None chromosome 5256310 5257263 + UV-endonuclease (UvsE/Uve1/UvdE Family) (NCBI ptt file) False
BC5390 BC5390 CDS None chromosome 5307293 5307715 + Cell wall hydrolase cwlJ (NCBI ptt file) False
BC5391 BC5391 CDS None chromosome 5307743 5308171 + hypothetical protein (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 351

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.