Organism : Bacillus cereus ATCC14579 | Module List:
Module 284 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 284

There are 9 regulatory influences for Module 284

Regulator Table (9)
Regulator Name Type
BC4652 tf
BC3653 tf
BC3194 tf
BC0122 tf
BC0958 tf
BC0473 tf
BC3163 tf
BC0598 tf
BC3814 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
4484 1.70e-06 CtcCCC
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4485 6.80e+03 TCcCCtaCTT
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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 284 is enriched for following functions.

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 8.70e-03 1.12e-02 3/35

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 284

There are 35 genes in Module 284

Gene Member Table (35)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
BC0637 BC0637 CDS None chromosome 633842 634813 + putative protein kinase (NCBI ptt file) False
BC0699 BC0699 CDS None chromosome 698715 700130 - Arginine permease (NCBI ptt file) False
BC0958 BC0958 CDS None chromosome 946144 946917 - Transcriptional regulator (NCBI ptt file) True
BC1052 BC1052 CDS None chromosome 1031164 1031871 + Protein ecsC (NCBI ptt file) False
BC1084 BC1084 CDS None chromosome 1070986 1071114 - hypothetical protein (NCBI ptt file) False
BC1123 BC1123 CDS None chromosome 1103270 1104538 + Zinc metalloprotease (NCBI ptt file) False
BC1176 BC1176 CDS None chromosome 1155369 1156115 + hypothetical protein (NCBI ptt file) False
BC1186 BC1186 CDS None chromosome 1167894 1168097 - hypothetical protein (NCBI ptt file) False
BC1339 BC1339 CDS None chromosome 1316796 1317314 + hypothetical protein (NCBI ptt file) False
BC1366 BC1366 CDS None chromosome 1335277 1335675 + SSEB protein (NCBI ptt file) False
BC1367 BC1367 CDS None chromosome 1335703 1336623 - Muramoyltetrapeptide carboxypeptidase (NCBI ptt file) False
BC1518 BC1518 CDS None chromosome 1471013 1472125 + Histidinol-phosphate aminotransferase (NCBI ptt file) False
BC1695 BC1695 CDS None chromosome 1643283 1643693 - Transcriptional regulator, MarR family (NCBI ptt file) True
BC1958 BC1958 CDS None chromosome 1906235 1906963 + 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) False
BC1989 BC1989 CDS None chromosome 1937268 1938233 - hypothetical Membrane Spanning Protein (NCBI ptt file) False
BC2017 BC2017 CDS None chromosome 1962284 1962877 + Ribosomal-protein-serine acetyltransferase (NCBI ptt file) False
BC2032 BC2032 CDS None chromosome 1975839 1976456 + Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) False
BC2186 BC2186 CDS None chromosome 2133477 2134064 + hypothetical protein (NCBI ptt file) False
BC2209 BC2209 CDS None chromosome 2154711 2155586 + D-amino acid aminotransferase (RefSeq) False
BC2265 BC2265 CDS None chromosome 2210357 2210608 + hypothetical protein (NCBI ptt file) False
BC2642 BC2642 DUMMY None chromosome 0 0 + None False
BC2729 BC2729 CDS None chromosome 2704132 2705172 - Penicillin-binding protein (NCBI ptt file) False
BC2944 BC2944 CDS None chromosome 2904286 2904435 - hypothetical protein (NCBI ptt file) False
BC2959 BC2959 CDS None chromosome 2916289 2917782 + Malate:quinone oxidoreductase (NCBI ptt file) False
BC3607 BC3607 CDS None chromosome 3583667 3584959 + spore peptidoglycan hydrolase (N-acetylglucosaminidase) (NCBI ptt file) False
BC4354 BC4354 CDS None chromosome 4295747 4296604 - Glyoxalase family protein (NCBI ptt file) False
BC4565 BC4565 CDS None chromosome 4511602 4512360 + CAAX amino terminal protease family (NCBI ptt file) False
BC4908 BC4908 CDS None chromosome 4820090 4820266 - hypothetical Membrane Associated Protein (NCBI ptt file) False
BC4951 BC4951 CDS None chromosome 4866631 4866930 - hypothetical protein (NCBI ptt file) False
BC5006 BC5006 CDS None chromosome 4911269 4912186 - Prolyne dehydrogenase (NCBI ptt file) False
BC5014 BC5014 CDS None chromosome 4919779 4920066 - hypothetical exported repetitive protein (NCBI ptt file) False
BC5045 BC5045 CDS None chromosome 4949759 4949956 + hypothetical protein (NCBI ptt file) False
BC5046 BC5046 CDS None chromosome 4950358 4950936 - Lysine decarboxylase family (NCBI ptt file) False
BC5284 BC5284 CDS None chromosome 5194047 5194751 - ABC transporter permease protein (NCBI ptt file) False
BC5333 BC5333 CDS None chromosome 5239820 5240785 - Fructose-1,6-bisphosphatase (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 284

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.