Organism : Bacillus cereus ATCC14579 | Module List:
Module 449 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 449

There are 16 regulatory influences for Module 449

Regulator Table (16)
Regulator Name Type
BC0993 tf
BC2386 tf
BC5340 tf
BC0851 tf
BC3072 tf
BC5097 tf
BC0758 tf
BC0114 tf
BC1732 tf
BC0882 tf
BC4212 tf
BC3756 tf
BC1889 tf
BC4505 tf
BC3438 tf
BC4073 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
4808 2.80e-02 aaAgggAG
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4809 2.20e+04 cTgaTgctgCgc.a.tA.gtgttA
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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 449 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 1.62e-02 3.42e-02 4/46

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transcription cog subcategory 7.77e-03 1.35e-02 7/46
Signal transduction mechanisms cog subcategory 2.03e-02 3.32e-02 4/46
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 449

There are 46 genes in Module 449

Gene Member Table (46)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0234 BC0234 CDS None chromosome 208346 209110 + Sec-independent secretion TatD (NCBI ptt file) False
BC0388 BC0388 CDS None chromosome 368371 368601 + hypothetical protein (NCBI ptt file) False
BC0392 BC0392 CDS None chromosome 370892 372157 + hypothetical protein (NCBI ptt file) False
BC0425 BC0425 CDS None chromosome 414386 415153 + Hydroxymethylpyrimidine transport system permease protein (NCBI ptt file) False
BC0426 BC0426 CDS None chromosome 415150 416148 + Hydroxymethylpyrimidine-binding protein (NCBI ptt file) False
BC0752 BC0752 CDS None chromosome 737848 738165 + hypothetical protein (NCBI ptt file) False
BC0788 BC0788 CDS None chromosome 773101 774372 + hypothetical protein (NCBI ptt file) False
BC0790 BC0790 CDS None chromosome 775484 775870 + hypothetical protein (NCBI ptt file) False
BC0839 BC0839 CDS None chromosome 818032 818346 + hypothetical protein (NCBI ptt file) False
BC0851 BC0851 CDS None chromosome 827758 828117 + Mercuric resistance operon regulatory protein (NCBI ptt file) True
BC0879 BC0879 CDS None chromosome 856814 857959 + hypothetical Membrane Associated Protein (NCBI ptt file) False
BC1095 BC1095 CDS None chromosome 1079919 1080506 - hypothetical protein (NCBI ptt file) False
BC1294 BC1294 CDS None chromosome 1272527 1273144 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1319 BC1319 CDS None chromosome 1295234 1296421 + Oxidoreductase (NCBI ptt file) False
BC1807 BC1807 CDS None chromosome 1762823 1764649 + Amino acid permease (NCBI ptt file) False
BC1931 BC1931 CDS None chromosome 1875863 1876864 + Branched-chain amino acid transport system permease protein livM (NCBI ptt file) False
BC2262 BC2262 CDS None chromosome 2208187 2208519 - Thioredoxin (NCBI ptt file) False
BC2351 BC2351 CDS None chromosome 2298703 2299263 + Transcriptional regulator, MerR family (NCBI ptt file) True
BC2386 BC2386 CDS None chromosome 2330497 2331366 + RNA polymerase ECF-type sigma factor (NCBI ptt file) True
BC2388 BC2388 CDS None chromosome 2331847 2332455 + Caffeoyl-CoA O-methyltransferase (NCBI ptt file) False
BC2476 BC2476 CDS None chromosome 2446150 2446992 + phosphoesterase (NCBI ptt file) False
BC2520 BC2520 CDS None chromosome 2493115 2493909 + Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (NCBI ptt file) False
BC2538 BC2538 CDS None chromosome 2511158 2511865 + Two-component response regulator yxdJ (NCBI ptt file) False
BC2578 BC2578 CDS None chromosome 2545594 2545989 + Phage protein (NCBI ptt file) False
BC2691 BC2691 CDS None chromosome 2674785 2675210 + Acetyltransferase (NCBI ptt file) False
BC2955 BC2955 CDS None chromosome 2913258 2913422 + hypothetical protein (NCBI ptt file) False
BC3072 BC3072 CDS None chromosome 3027936 3028643 - Transcriptional regulator, ArsR family (NCBI ptt file) True
BC3118 BC3118 CDS None chromosome 3085877 3086137 - Cytochrome p450 (NCBI ptt file) False
BC3200 BC3200 CDS None chromosome 3175320 3175994 + Two-component response regulator (NCBI ptt file) False
BC3226 BC3226 CDS None chromosome 3207981 3208451 - hypothetical protein (NCBI ptt file) False
BC3252 BC3252 CDS None chromosome 3231492 3231743 - hypothetical protein (NCBI ptt file) False
BC3490 BC3490 CDS None chromosome 3445904 3447031 - Penicillin-binding protein (NCBI ptt file) False
BC3756 BC3756 CDS None chromosome 3720127 3721560 - Transcriptional regulator, GntR family (NCBI ptt file) True
BC3985 BC3985 CDS None chromosome 3960729 3961247 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC4246 BC4246 CDS None chromosome 4191530 4192063 - hypothetical protein (NCBI ptt file) False
BC4334 BC4334 CDS None chromosome 4274980 4275135 + hypothetical protein (NCBI ptt file) False
BC4373 BC4373 CDS None chromosome 4312793 4313491 - hypothetical protein (NCBI ptt file) False
BC4416 BC4416 CDS None chromosome 4357135 4358079 + Ferrichrome-binding protein (NCBI ptt file) False
BC4495 BC4495 CDS None chromosome 4440619 4441668 - Germination protein germ (NCBI ptt file) False
BC4809 BC4809 CDS None chromosome 4733728 4735581 - Two component system histidine kinase (NCBI ptt file) False
BC4848 BC4848 CDS None chromosome 4771537 4772643 - Sensor protein vanS (NCBI ptt file) False
BC4975 BC4975 CDS None chromosome 4882204 4882935 - hypothetical Membrane Associated Protein (NCBI ptt file) False
BC5094 BC5094 CDS None chromosome 4999000 4999227 - Transposase (NCBI ptt file) False
BC5096 BC5096 CDS None chromosome 4999413 4999556 - hypothetical protein (NCBI ptt file) False
BC5287 BC5287 CDS None chromosome 5196883 5197917 - Stage II sporulation protein D (NCBI ptt file) False
BC5340 BC5340 CDS None chromosome 5247271 5247900 - Transcriptional regulator, TetR family (NCBI ptt file) True

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 449

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.