Organism : Bacillus cereus ATCC14579 | Module List:
Module 186 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 186

There are 2 regulatory influences for Module 186

Regulator Table (2)
Regulator Name Type
BC2964 tf
BC3982 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
4288 5.80e-05 ttCC.ccTtC
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4289 2.40e+00 aAGGAGg
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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 186 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 186

There are 40 genes in Module 186

Gene Member Table (40)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0581 BC0581 CDS None chromosome 567147 567671 - hypothetical protein (NCBI ptt file) False
BC1206 BC1206 CDS None chromosome 1186805 1187650 - Macrocin O-methyltransferase (NCBI ptt file) False
BC1218 BC1218 CDS None chromosome 1196731 1197189 - Spore coat protein Y (NCBI ptt file) False
BC1245 BC1245 CDS None chromosome 1220087 1220518 - hypothetical protein (NCBI ptt file) False
BC1445 BC1445 CDS None chromosome 1404671 1404868 - hypothetical protein (NCBI ptt file) False
BC1539 BC1539 CDS None chromosome 1488623 1488796 - hypothetical protein (NCBI ptt file) False
BC1573 BC1573 CDS None chromosome 1522761 1523015 - hypothetical protein (NCBI ptt file) False
BC1706 BC1706 CDS None chromosome 1654715 1655560 + hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC1714 BC1714 CDS None chromosome 1662574 1662693 - hypothetical protein (NCBI ptt file) False
BC1805 BC1805 CDS None chromosome 1759604 1761079 - hypothetical protein (NCBI ptt file) False
BC1808 BC1808 CDS None chromosome 1764734 1764937 - hypothetical protein (NCBI ptt file) False
BC1895 BC1895 CDS None chromosome 1840246 1840470 + Phage protein (NCBI ptt file) False
BC1901 BC1901 CDS None chromosome 1842812 1843318 + Phage protein (NCBI ptt file) False
BC1929 BC1929 CDS None chromosome 1874278 1874979 + Branched-chain amino acid transport ATP-binding protein livF (NCBI ptt file) False
BC2007 BC2007 CDS None chromosome 1954623 1954784 - hypothetical protein (NCBI ptt file) False
BC2091 BC2091 CDS None chromosome 2036383 2036640 - hypothetical protein (NCBI ptt file) False
BC2098 BC2098 CDS None chromosome 2041598 2041813 + hypothetical protein (NCBI ptt file) False
BC2244 BC2244 CDS None chromosome 2192727 2193476 - hypothetical protein (NCBI ptt file) False
BC2282 BC2282 CDS None chromosome 2224755 2225039 - hypothetical protein (NCBI ptt file) False
BC2647 BC2647 CDS None chromosome 2630095 2630502 - hypothetical protein (NCBI ptt file) False
BC2712 BC2712 CDS None chromosome 2690914 2691120 + hypothetical protein (NCBI ptt file) False
BC2762 BC2762 CDS None chromosome 2738698 2739501 + hypothetical protein (NCBI ptt file) False
BC2965 BC2965 CDS None chromosome 2923413 2924981 + Sugar (pentulose and hexulose) kinases (NCBI ptt file) False
BC2994 BC2994 CDS None chromosome 2952324 2952569 + hypothetical protein (NCBI ptt file) False
BC3099 BC3099 CDS None chromosome 3055914 3057413 - Spore germination protein QA (NCBI ptt file) False
BC3145 BC3145 CDS None chromosome 3116700 3116900 - hypothetical protein (NCBI ptt file) False
BC3147 BC3147 CDS None chromosome 3117956 3118279 - hypothetical protein (NCBI ptt file) False
BC3172 BC3172 CDS None chromosome 3142711 3142956 - hypothetical protein (NCBI ptt file) False
BC3357 BC3357 CDS None chromosome 3320285 3321058 + hypothetical protein (NCBI ptt file) False
BC3397 BC3397 CDS None chromosome 3362428 3362616 + hypothetical protein (NCBI ptt file) False
BC3579 BC3579 CDS None chromosome 3553383 3555482 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC3598 BC3598 CDS None chromosome 3576698 3576913 + hypothetical protein (NCBI ptt file) False
BC3652 BC3652 CDS None chromosome 3623637 3625157 - Histidine ammonia-lyase (NCBI ptt file) False
BC3750 BC3750 CDS None chromosome 3715730 3716716 - UDP-N-acetylglucosamine 4,6-dehydratase (NCBI ptt file) False
BC4595 BC4595 CDS None chromosome 4541700 4541918 + hypothetical protein (NCBI ptt file) False
BC4862 BC4862 CDS None chromosome 4785528 4786250 + Lipase (NCBI ptt file) False
BC4916 BC4916 CDS None chromosome 4826713 4827456 + hypothetical Cytosolic Protein (NCBI ptt file) False
BC5134 BC5134 CDS None chromosome 5036708 5037658 + Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) False
BC5247 BC5247 CDS None chromosome 5158160 5158384 + hypothetical protein (NCBI ptt file) False
BC5360 BC5360 CDS None chromosome 5279684 5280133 + 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 186

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.