Organism : Bacillus cereus ATCC14579 | Module List:
Module 105 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 105

There are 17 regulatory influences for Module 105

Regulator Table (17)
Regulator Name Type
BC0586 tf
BC3922 tf
BC1531 tf
BC2794 tf
BC1490 tf
BC1296 tf
BC5205 tf
BC3706 tf
BC4174 tf
BC4834 tf
BC0954 tf
BC4211 tf
BC4081 tf
BC4968 tf
BC4832 tf
BC5265 tf
BC1489 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
4126 6.30e-01 CCtCCTttatt
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4127 1.40e+04 gtGggAAGCG
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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 105 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Global kegg category 1.74e-02 3.57e-02 7/26
Metabolism kegg subcategory 1.74e-02 3.57e-02 7/26
Metabolic pathways kegg pathway 9.32e-03 2.28e-02 7/26
Biosynthesis of secondary metabolites kegg pathway 1.51e-02 3.23e-02 4/26

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 5.17e-03 9.24e-03 12/26
Poorly characterized cog category 1.74e-02 2.89e-02 8/26
Carbohydrate transport and metabolism cog subcategory 2.18e-02 3.54e-02 3/26
Amino acid transport and metabolism cog subcategory 2.89e-02 4.61e-02 4/26
Nucleotide transport and metabolism cog subcategory 1.18e-03 2.32e-03 3/26
General function prediction only cog subcategory 1.62e-03 3.11e-03 7/26
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 105

There are 26 genes in Module 105

Gene Member Table (26)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0476 BC0476 CDS None chromosome 466349 467569 + Acetylornithine deacetylase (NCBI ptt file) False
BC0597 BC0597 CDS None chromosome 587623 589086 - Nicotinate phosphoribosyltransferase (NCBI ptt file) False
BC1111 BC1111 CDS None chromosome 1092751 1093857 + phosphoesterase (NCBI ptt file) False
BC1923 BC1923 CDS None chromosome 1867245 1868258 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC2232 BC2232 CDS None chromosome 2177843 2178790 + Glycine betaine transport ATP-binding protein (NCBI ptt file) False
BC2233 BC2233 CDS None chromosome 2178794 2180305 + Glycine betaine transport system permease protein / Glycine betaine-binding protein (NCBI ptt file) False
BC2793 BC2793 CDS None chromosome 2761646 2762227 - ATP-dependent Clp protease proteolytic subunit (NCBI ptt file) False
BC2794 BC2794 CDS None chromosome 2762249 2762935 - RNA polymerase ECF-type sigma factor (NCBI ptt file) True
BC3045 BC3045 CDS None chromosome 3003545 3004369 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC3369 BC3369 CDS None chromosome 3330421 3331962 - Gluconokinase (NCBI ptt file) False
BC3370 BC3370 CDS None chromosome 3332093 3333418 - Gluconate permease (NCBI ptt file) False
BC3371 BC3371 CDS None chromosome 3333815 3334483 - Transaldolase (NCBI ptt file) False
BC3373 BC3373 DUMMY None chromosome 0 0 + None False
BC3416 BC3416 CDS None chromosome 3379060 3379809 - SMS protein (NCBI ptt file) False
BC3673 BC3673 CDS None chromosome 3639793 3640548 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC3786 BC3786 CDS None chromosome 3757584 3758870 - Zinc protease (NCBI ptt file) False
BC3787 BC3787 CDS None chromosome 3758871 3760145 - Zinc protease (NCBI ptt file) False
BC4502 BC4502 CDS None chromosome 4447594 4448880 - Xanthine permease (NCBI ptt file) False
BC4503 BC4503 CDS None chromosome 4448987 4450228 - Cytosine deaminase (NCBI ptt file) False
BC4624 fabG CDS None chromosome 4567836 4568627 - 3-ketoacyl-(acyl-carrier-protein) reductase (RefSeq) False
BC4915 BC4915 CDS None chromosome 4826234 4826617 - ComA operon protein 2 (NCBI ptt file) False
BC4977 BC4977 CDS None chromosome 4883358 4884638 - 5'-nucleotidase (NCBI ptt file) False
BC5319 BC5319 CDS None chromosome 5227364 5227804 - Protein tyrosine phosphatase (NCBI ptt file) False
BC5398 BC5398 CDS None chromosome 5312895 5313572 - Uracil-DNA glycosylase (NCBI ptt file) False
BC5401 BC5401 CDS None chromosome 5315491 5316300 - Lipase/Acylhydrolase with GDSL-like motif (NCBI ptt file) False
VIMSS12791521 VIMSS12791521 DUMMY None chromosome 0 0 + None 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 105

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.