Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 215 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 215

There are 9 regulatory influences for Module 215

Regulator Table (9)
Regulator Name Type
RSP_1191 tf
RSP_3680 tf
RSP_0623 tf
RSP_0547 tf
RSP_3385 tf
RSP_0611 tf
RSP_1776 tf
RSP_0014 tf
RSP_1518 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
8150 1.90e+01 ctGaTcgacATCGACgAgctcaA
Loader icon
8151 1.20e+04 aaCtGACGGTCGa
Loader icon
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 215 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell wall/membrane/envelope biogenesis cog subcategory 2.60e-02 3.99e-02 3/30
Coenzyme transport and metabolism cog subcategory 2.71e-02 4.15e-02 3/30
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 215

There are 30 genes in Module 215

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0014 RSP_0014 CDS None chromosome 1 1715549 1716166 + transcriptional regulator, TetR family (NCBI) True
RSP_0337 RSP_0337 CDS None chromosome 1 2067539 2068360 - possible phospodiesterase (NCBI) False
RSP_0338 RSP_0338 CDS None chromosome 1 2068357 2069274 - hypothetical protein (NCBI) False
RSP_0363 RSP_0363 CDS None chromosome 1 2094117 2094815 - hypothetical protein (NCBI) False
RSP_0586 RSP_0586 CDS None chromosome 1 2329105 2329674 - probable nicotinate-nucleotide adenylyltransferase (NCBI) False
RSP_0782 RSP_0782 CDS None chromosome 1 2526699 2528240 + Ppx/GppA phosphatase (NCBI) False
RSP_0784 RSP_0784 CDS None chromosome 1 2528862 2529338 + putative acetyltransferase, GNAT family (NCBI) False
RSP_0814 RSP_0814 CDS None chromosome 1 2555865 2556578 - Acetyltransferase (NCBI) False
RSP_1189 wcaJ CDS None chromosome 1 2963295 2963939 - sugar transferase (NCBI) False
RSP_1190 RSP_1190 CDS None chromosome 1 2963936 2964769 - hypothetical protein (NCBI) False
RSP_1191 RSP_1191 CDS None chromosome 1 2964769 2965212 - transcriptional regulator, MarR family (NCBI) True
RSP_1192 RSP_1192 DUMMY None chromosome 1 0 0 + None False
RSP_1214 RSP_1214 CDS None chromosome 1 2984836 2985558 - putative branched-chain amino acid aminotransferase (NCBI) False
RSP_1275 RSP_1275 CDS None chromosome 1 3043116 3043865 + Crp-Fnr family transciptional regulator (NCBI) False
RSP_1276 RSP_1276 CDS None chromosome 1 3044005 3044457 + hypothetical protein (NCBI) False
RSP_1287 RSP_1287 CDS None chromosome 1 3054495 3055190 - ABC branched chain amino acid family transporter, ATPase subunit (NCBI) False
RSP_1369 RSP_1369 CDS None chromosome 1 3146893 3147675 + Short-chain dehydrogenase/reductase SDR (NCBI) False
RSP_1511 RSP_1511 CDS None chromosome 1 98604 98876 + hypothetical protein (NCBI) False
RSP_1861 RSP_1861 CDS None chromosome 1 459590 460492 + probable dihydroneopterin aldolase (NCBI) False
RSP_2312 RSP_2312 CDS None chromosome 1 934513 935088 - hypothetical protein (NCBI) False
RSP_2375 RSP_2375 CDS None chromosome 1 1002024 1003469 + hypothetical protein (NCBI) False
RSP_2382 RSP_2382 CDS None chromosome 1 1011405 1012514 - hypothetical protein (NCBI) False
RSP_2391 RSP_2391 CDS None chromosome 1 1019816 1020370 + 2'-5' RNA ligase (NCBI) False
RSP_2634 ccmH CDS None chromosome 1 1274996 1275451 + Cytochrome c maturation protein, CcmH (NCBI) False
RSP_2678 RSP_2678 CDS None chromosome 1 1322934 1323188 - hypothetical protein (NCBI) False
RSP_2788 RSP_2788 CDS None chromosome 1 1434945 1435232 + hypothetical protein (NCBI) False
RSP_3023 RSP_3023 CDS None chromosome 2 53953 54858 - hypothetical protein (NCBI) False
RSP_3402 RSP_3402 CDS None chromosome 2 466542 469187 + multisensor diguanylate cyclase/phosphodiesterase (NCBI) False
RSP_3564 RSP_3564 CDS None chromosome 2 659453 660088 + Generic methyltransferase (NCBI) False
RSP_3680 RSP_3680 CDS None chromosome 2 800591 801214 - transcriptional regulator, TetR family (NCBI) True

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 215

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.