Organism : Bacillus cereus ATCC14579 | Module List:
Module 20 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 20

There are 15 regulatory influences for Module 20

Regulator Table (15)
Regulator Name Type
BC3493 tf
BC5251 tf
BC3244 tf
BC1889 tf
BC1363 tf
BC0114 tf
BC3983 tf
BC4826 tf
BC5402 tf
BC3592 tf
BC1818 tf
BC2217 tf
BC4010 tf
BC0801 tf
BC2444 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
3962 3.10e+02 taa.gaagagGA.GAaaaaaagaa
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3963 2.40e+04 CGCCCc
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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 20 is enriched for following functions.

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 20

There are 32 genes in Module 20

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0349 BC0349 CDS None chromosome 327205 327441 + hypothetical protein (NCBI ptt file) False
BC0360 BC0360 CDS None chromosome 338622 339851 - Aminopeptidase (NCBI ptt file) False
BC0766 BC0766 CDS None chromosome 751478 752473 - Methylthioribose transport system permease protein (NCBI ptt file) False
BC0781 BC0781 CDS None chromosome 765656 766168 - hypothetical protein (NCBI ptt file) False
BC0986 BC0986 CDS None chromosome 971287 972396 + Response regulator aspartate phosphatase (NCBI ptt file) False
BC1172 BC1172 CDS None chromosome 1151244 1151420 + ComZ protein (NCBI ptt file) False
BC1178 BC1178 CDS None chromosome 1157861 1158241 - hypothetical protein (NCBI ptt file) False
BC1431 BC1431 CDS None chromosome 1391058 1392323 - Cell wall endopeptidase, family M23/M37 (NCBI ptt file) False
BC1624 BC1624 CDS None chromosome 1580915 1581517 - hydrolase (HAD superfamily) (NCBI ptt file) False
BC1769 BC1769 CDS None chromosome 1722622 1722885 + hypothetical protein (NCBI ptt file) False
BC1889 BC1889 CDS None chromosome 1833383 1833763 + Phage protein (NCBI ptt file) True
BC2243 BC2243 DUMMY None chromosome 0 0 + None False
BC2364 BC2364 CDS None chromosome 2309113 2309544 - hypothetical protein (NCBI ptt file) False
BC2671 BC2671 CDS None chromosome 2654859 2655467 + ThiJ/PfpI family (NCBI ptt file) False
BC2675 BC2675 CDS None chromosome 2659753 2660556 + Acetyltransferase (NCBI ptt file) False
BC2749 BC2749 CDS None chromosome 2728518 2729015 - Acetyltransferase (NCBI ptt file) False
BC2750 BC2750 CDS None chromosome 2729042 2729398 - hypothetical protein (NCBI ptt file) False
BC2797 BC2797 CDS None chromosome 2764180 2764614 + Acetyltransferase (NCBI ptt file) False
BC2809 BC2809 CDS None chromosome 2772912 2773424 - Phosphinothricin N-acetyltransferase (NCBI ptt file) False
BC3421 BC3421 CDS None chromosome 3383613 3383936 + Transcriptional regulator, MarR family (NCBI ptt file) True
BC3460 BC3460 CDS None chromosome 3416153 3416896 + Short chain dehydrogenase (NCBI ptt file) False
BC3518 BC3518 CDS None chromosome 3475275 3476390 + Response regulator aspartate phosphatase (NCBI ptt file) False
BC3592 BC3592 CDS None chromosome 3568716 3569309 + Transcriptional regulator, TetR family (NCBI ptt file) True
BC3996 BC3996 CDS None chromosome 3971419 3972081 - hypothetical Exported Protein (NCBI ptt file) False
BC4035 BC4035 CDS None chromosome 4008933 4010111 + Aspartate aminotransferase (NCBI ptt file) False
BC4123 BC4123 CDS None chromosome 4088327 4089106 + Lipase/Acylhydrolase with GDSL-like motif (NCBI ptt file) False
BC4146 BC4146 CDS None chromosome 4111747 4112307 - Protein erfK/srfK precursor (NCBI ptt file) False
BC4908 BC4908 CDS None chromosome 4820090 4820266 - hypothetical Membrane Associated Protein (NCBI ptt file) False
BC4929 BC4929 CDS None chromosome 4849102 4850349 + Macrolide-efflux protein (NCBI ptt file) False
BC4931 BC4931 CDS None chromosome 4851328 4851789 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC4947 BC4947 CDS None chromosome 4863533 4864177 + hypothetical protein (NCBI ptt file) False
BC5046 BC5046 CDS None chromosome 4950358 4950936 - Lysine decarboxylase family (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 20

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.