Organism : Bacillus cereus ATCC14579 | Module List:
Module 511 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 511

There are 20 regulatory influences for Module 511

Regulator Table (20)
Regulator Name Type
BC4001 tf
BC2340 tf
BC1296 tf
BC0433 tf
BC3404 tf
BC1490 tf
BC0856 tf
BC3194 tf
BC3668 tf
BC1715 tf
BC4073 tf
BC2386 tf
BC2480 tf
BC5097 tf
BC1356 tf
BC2794 tf
BC0586 tf
BC0613 tf
BC5175 tf
BC1047 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
4932 2.90e-02 AAGgAGg
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4933 4.40e+03 ctcacCccTC
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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 511 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 511

There are 28 genes in Module 511

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0191 BC0191 CDS None chromosome 165423 166550 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC0424 BC0424 CDS None chromosome 414088 414408 + IG hypothetical 16092 (NCBI ptt file) False
BC1095 BC1095 CDS None chromosome 1079919 1080506 - hypothetical protein (NCBI ptt file) False
BC1193 BC1193 CDS None chromosome 1173833 1175659 + Oligoendopeptidase F (NCBI ptt file) False
BC1307 BC1307 CDS None chromosome 1286531 1286887 + hypothetical protein (NCBI ptt file) False
BC1415 BC1415 CDS None chromosome 1375728 1376699 + Glyoxylate reductase (NADP+) (NCBI ptt file) False
BC2101 BC2101 CDS None chromosome 2043162 2044850 + Formate--tetrahydrofolate ligase (NCBI ptt file) False
BC2156 BC2156 CDS None chromosome 2099430 2099813 + Thioredoxin (NCBI ptt file) False
BC2158 BC2158 CDS None chromosome 2100381 2101157 + Protein-L-isoD(D-D) O-methyltransferase (NCBI ptt file) False
BC2241 BC2241 CDS None chromosome 2189404 2190828 + Succinate-semialdehyde dehydrogenase [NADP+] (NCBI ptt file) False
BC2293 BC2293 CDS None chromosome 2237300 2237557 + hypothetical protein (NCBI ptt file) False
BC2371 BC2371 CDS None chromosome 2315113 2316867 + Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) False
BC2479 BC2479 CDS None chromosome 2448370 2449383 + ABC transporter permease protein (NCBI ptt file) False
BC2556 BC2556 CDS None chromosome 2530048 2531157 - DNA integration/recombination/invertion protein (NCBI ptt file) False
BC2616 BC2616 CDS None chromosome 2578357 2578659 + Cytochrome P450(MEG) (NCBI ptt file) False
BC2954 BC2954 CDS None chromosome 2912684 2913073 + Lactoylglutathione lyase (NCBI ptt file) False
BC2955 BC2955 CDS None chromosome 2913258 2913422 + hypothetical protein (NCBI ptt file) False
BC3026 BC3026 CDS None chromosome 2987348 2989291 + Tetracycline resistance protein tetP (NCBI ptt file) False
BC3143 BC3143 CDS None chromosome 3116195 3116320 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3144 BC3144 CDS None chromosome 3116403 3116558 - hypothetical Cytosolic Protein (NCBI ptt file) False
BC3194 BC3194 CDS None chromosome 3168963 3169382 - Transcriptional regulator, MarR family (NCBI ptt file) True
BC4019 BC4019 CDS None chromosome 3996164 3996595 + hypothetical protein (NCBI ptt file) False
BC4084 BC4084 CDS None chromosome 4052285 4053235 - Magnesium and cobalt transport protein corA (NCBI ptt file) False
BC4092 BC4092 CDS None chromosome 4059676 4060323 - Stage II sporulation protein M (NCBI ptt file) False
BC4098 BC4098 CDS None chromosome 4063794 4064318 - Glutamate-rich protein grpB (NCBI ptt file) False
BC4804 BC4804 CDS None chromosome 4730069 4730242 - hypothetical protein (NCBI ptt file) False
BC4807 BC4807 CDS None chromosome 4732242 4732469 - Ferrous iron transport protein A (NCBI ptt file) False
BC5279 BC5279 CDS None chromosome 5189074 5189757 - Tyrosine-protein kinase (capsular polysaccharide biosynthesis) (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 511

Please add your comments for this module by using the form below. Your comments will be publicly available.

comments powered by Disqus
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.