Organism : Bacillus cereus ATCC14579 | Module List:
Module 334 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 334

There are 5 regulatory influences for Module 334

Regulator Table (5)
Regulator Name Type
BC3653 tf
BC2680 tf
BC2964 tf
BC2837 tf
BC1851 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
4580 1.70e-04 T.CCcCctTcattaT
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4581 6.70e+02 aaaGGaGG
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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 334 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 334

There are 35 genes in Module 334

Gene Member Table (35)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0823 BC0823 CDS None chromosome 806934 807149 - CotJA protein (NCBI ptt file) False
BC0878 BC0878 CDS None chromosome 855641 856702 - IG hypothetical 16724 (NCBI ptt file) False
BC0904 BC0904 CDS None chromosome 892794 893105 - hypothetical protein (NCBI ptt file) False
BC1429 BC1429 CDS None chromosome 1389111 1389254 - hypothetical protein (NCBI ptt file) False
BC1573 BC1573 CDS None chromosome 1522761 1523015 - 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
BC1894 BC1894 CDS None chromosome 1839072 1840196 + Phage protein (NCBI ptt file) False
BC1905 BC1905 CDS None chromosome 1844399 1844692 + Phage protein (NCBI ptt file) False
BC1911 BC1911 CDS None chromosome 1855674 1856738 + N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) False
BC1928 BC1928 CDS None chromosome 1873535 1874278 + Branched-chain amino acid transport ATP-binding protein livG (NCBI ptt file) False
BC2007 BC2007 CDS None chromosome 1954623 1954784 - hypothetical protein (NCBI ptt file) False
BC2010 BC2010 CDS None chromosome 1955783 1956823 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC2091 BC2091 CDS None chromosome 2036383 2036640 - hypothetical protein (NCBI ptt file) False
BC2149 BC2149 CDS None chromosome 2092910 2093737 - hypothetical protein (NCBI ptt file) False
BC2383 BC2383 CDS None chromosome 2327951 2328151 - Oxalate decarboxylase (NCBI ptt file) False
BC2509 BC2509 CDS None chromosome 2479222 2480022 + Sortase (NCBI ptt file) False
BC2712 BC2712 CDS None chromosome 2690914 2691120 + hypothetical protein (NCBI ptt file) False
BC2753 BC2753 CDS None chromosome 2731485 2732264 - Cell wall hydrolase cwlJ (NCBI ptt file) False
BC2875 BC2875 CDS None chromosome 2835396 2835551 - hypothetical protein (NCBI ptt file) False
BC2962 BC2962 CDS None chromosome 2919856 2920809 - Sugar transport system permease protein (NCBI ptt file) False
BC2981 BC2981 CDS None chromosome 2940322 2940495 + hypothetical protein (NCBI ptt file) False
BC3360 BC3360 CDS None chromosome 3323011 3324234 + Methyltransferase (NCBI ptt file) False
BC3397 BC3397 CDS None chromosome 3362428 3362616 + hypothetical protein (NCBI ptt file) False
BC3598 BC3598 CDS None chromosome 3576698 3576913 + hypothetical protein (NCBI ptt file) False
BC3733 BC3733 CDS None chromosome 3698087 3698314 - hypothetical protein (NCBI ptt file) False
BC3751 BC3751 CDS None chromosome 3717019 3718197 + hypothetical protein (NCBI ptt file) False
BC4002 BC4002 CDS None chromosome 3977069 3977257 - hypothetical protein (NCBI ptt file) False
BC4070 BC4070 CDS None chromosome 4039907 4040527 - Stage V sporulation protein AA (NCBI ptt file) False
BC4171 BC4171 CDS None chromosome 4133398 4133595 + hypothetical protein (NCBI ptt file) False
BC4591 BC4591 CDS None chromosome 4537372 4537845 - MaoC family protein (NCBI ptt file) False
BC4595 BC4595 CDS None chromosome 4541700 4541918 + hypothetical protein (NCBI ptt file) False
BC4635 BC4635 CDS None chromosome 4576558 4577193 + hypothetical protein (NCBI ptt file) False
BC4960 BC4960 CDS None chromosome 4872184 4872816 - Transcriptional regulator, DeoR family (NCBI ptt file) True
BC5134 BC5134 CDS None chromosome 5036708 5037658 + Inosine-uridine preferring nucleoside hydrolase (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 334

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.