Organism : Bacillus cereus ATCC14579 | Module List:
Module 122 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 122

There are 13 regulatory influences for Module 122

Regulator Table (13)
Regulator Name Type
BC0213 tf
BC0586 tf
BC4211 tf
BC3400 tf
BC2631 tf
BC4474 tf
BC4395 tf
BC4277 tf
BC3025 tf
BC4570 tf
BC4181 tf
BC1302 tf
BC3976 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
4160 1.60e+02 gccCaattCaC
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4161 1.10e+03 AaaGGaGa
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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 122 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 9.60e-04 5.59e-03 9/22
Metabolism of Cofactors and Vitamins kegg subcategory 1.00e-05 2.10e-04 5/22
Porphyrin and chlorophyll metabolism kegg pathway 0.00e+00 0.00e+00 5/22
Environmental Information Processing kegg category 5.42e-03 1.59e-02 4/22
Membrane Transport kegg subcategory 1.25e-03 6.59e-03 4/22
ABC transporters kegg pathway 5.86e-04 4.12e-03 4/22
Global kegg category 5.80e-03 1.66e-02 7/22
Metabolism kegg subcategory 5.80e-03 1.66e-02 7/22
Metabolic pathways kegg pathway 2.96e-03 1.09e-02 7/22
Biosynthesis of secondary metabolites kegg pathway 1.63e-04 1.69e-03 6/22

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 5.89e-04 1.02e-03 3/22
Heme, porphyrin, and cobalamin tigr sub1role 1.00e-06 2.00e-06 3/22

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 9.94e-03 1.71e-02 10/22
Coenzyme transport and metabolism cog subcategory 2.20e-05 7.50e-05 5/22
Inorganic ion transport and metabolism cog subcategory 1.68e-03 3.21e-03 4/22
ABC-type Fe3+-siderophore transport system, permease component cog 0.00e+00 0.00e+00 3/22
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 122

There are 22 genes in Module 122

Gene Member Table (22)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0381 BC0381 CDS None chromosome 363215 364222 - Ferrichrome transport system permease protein fhuG (NCBI ptt file) False
BC0382 BC0382 CDS None chromosome 364219 365235 - Ferrichrome transport system permease protein fhuB (NCBI ptt file) False
BC0383 BC0383 CDS None chromosome 365308 366228 - Ferrichrome-binding protein (NCBI ptt file) False
BC1022 BC1022 CDS None chromosome 1002632 1002964 + hypothetical protein (NCBI ptt file) False
BC1495 BC1495 CDS None chromosome 1450114 1451094 + Thioredoxin reductase (NCBI ptt file) False
BC1557 BC1557 CDS None chromosome 1505045 1505389 + hypothetical protein (NCBI ptt file) False
BC3396 BC3396 CDS None chromosome 3361989 3362360 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC3958 BC3958 CDS None chromosome 3938305 3939090 - Myo-inositol-1(or 4)-monophosphatase (NCBI ptt file) False
BC4394 BC4394 CDS None chromosome 4332334 4333620 + ATPase, AAA family (NCBI ptt file) False
BC4395 BC4395 CDS None chromosome 4333643 4334299 + Prespore specific transcriptional activator rsfA (NCBI ptt file) True
BC4400 BC4400 CDS None chromosome 4339895 4340335 - D-tyrosyl-tRNA(Tyr) deacylase (NCBI ptt file) False
BC4401 BC4401 CDS None chromosome 4340352 4342535 - GTP pyrophosphokinase (NCBI ptt file) False
BC4468 BC4468 CDS None chromosome 4414627 4415916 - Glutamate-1-semialdehyde 2,1-aminomutase (NCBI ptt file) False
BC4469 BC4469 CDS None chromosome 4415916 4416905 - Delta-aminolevulinic acid dehydratase (NCBI ptt file) False
BC4470 BC4470 CDS None chromosome 4416926 4417678 - Uroporphyrinogen-III synthase (NCBI ptt file) False
BC4471 BC4471 CDS None chromosome 4417681 4418610 - Porphobilinogen deaminase (NCBI ptt file) False
BC4472 BC4472 CDS None chromosome 4418626 4419459 - HEMX protein (NCBI ptt file) False
BC4473 BC4473 CDS None chromosome 4419477 4420811 - Glutamyl-tRNA reductase (NCBI ptt file) False
BC4496 BC4496 CDS None chromosome 4441850 4442659 - Glutamate racemase (NCBI ptt file) False
BC4752 BC4752 CDS None chromosome 4687550 4688614 - hypothetical protein (NCBI ptt file) False
BC4994 BC4994 CDS None chromosome 4898197 4898844 + Ser/Thr and Tyr protein phosphatase (dual specificity) (NCBI ptt file) False
BC5382 BC5382 CDS None chromosome 5298927 5299943 - Ferrichrome transport system permease protein fhuG (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 122

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.