Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 225 Profile

GeneModule member RegulatorRegulator MotifMotif
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 225

There are 6 regulatory influences for Module 225

Regulator Table (6)
Regulator Name Type
RSP_3026 tf
RSP_1952 tf
RSP_0591 tf
RSP_1776 tf
RSP_1741 tf
RSP_2494 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
8168 4.00e-38 cCaaCTGAGCTAc
Loader icon
8169 3.70e-08 agaaatcg.cagattgcCtCTTGc
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 225 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Genetic Information Processing kegg category 0.00e+00 0.00e+00 27/28
Translation kegg subcategory 0.00e+00 0.00e+00 27/28
Aminoacyl-tRNA biosynthesis kegg pathway 0.00e+00 0.00e+00 27/28

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 225

There are 28 genes in Module 225

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_4296 RSP_4296 tRNA None chromosome 1 1843556 1843630 + tRNA-Gly (NCBI) False
RSP_4297 RSP_4297 tRNA None chromosome 1 675421 675497 - tRNA-Arg (NCBI) False
RSP_4299 RSP_4299 tRNA None chromosome 1 1920665 1920739 + tRNA-Asn (NCBI) False
RSP_4302 RSP_4302 tRNA None chromosome 1 215732 215821 - tRNA-Ser (NCBI) False
RSP_4303 RSP_4303 tRNA None chromosome 2 704742 704818 + tRNA-Met (NCBI) False
RSP_4304 RSP_4304 tRNA None chromosome 1 1807746 1807817 + tRNA-Thr (NCBI) False
RSP_4305 RSP_4305 tRNA None chromosome 1 1413287 1413360 - tRNA-Gly (NCBI) False
RSP_4306 RSP_4306 tRNA None chromosome 2 373306 373395 + tRNA-Ser (NCBI) False
RSP_4307 RSP_4307 tRNA None chromosome 1 5272 5348 + tRNA-Met (NCBI) False
RSP_4310 RSP_4310 tRNA None chromosome 1 255196 255271 - tRNA-Arg (NCBI) False
RSP_4312 RSP_4312 tRNA None chromosome 1 2139072 2139146 + tRNA-Glu (NCBI) False
RSP_4316 RSP_4316 tRNA None chromosome 1 1679031 1679107 - tRNA-Asp (NCBI) False
RSP_4318 RSP_4318 tRNA None chromosome 1 92706 92781 - tRNA-Thr (NCBI) False
RSP_4320 RSP_4320 tRNA None chromosome 1 2813672 2813748 - tRNA-Arg (NCBI) False
RSP_4322 RSP_4322 tRNA None chromosome 1 1852143 1852216 - tRNA-Cys (NCBI) False
RSP_4327 RSP_4327 tRNA None chromosome 1 1479346 1479420 + tRNA-Gln (NCBI) False
RSP_4328 RSP_4328 tRNA None chromosome 1 1508343 1508417 - tRNA-Val (NCBI) False
RSP_4329 RSP_4329 tRNA None chromosome 1 2687477 2687551 + tRNA-Lys (NCBI) False
RSP_4330 RSP_4330 tRNA None chromosome 1 2741730 2741805 + tRNA-Ala (NCBI) False
RSP_4331 RSP_4331 tRNA None chromosome 1 1251312 1251389 - tRNA-Pro (NCBI) False
RSP_4333 RSP_4333 tRNA None chromosome 1 2361949 2362024 - tRNA-Phe (NCBI) False
RSP_4334 RSP_4334 tRNA None chromosome 1 2344688 2344764 + tRNA-Arg (NCBI) False
RSP_4335 RSP_4335 tRNA None chromosome 1 2370733 2370807 + tRNA-Thr (NCBI) False
RSP_4336 RSP_4336 tRNA None chromosome 1 2495608 2495684 + tRNA-His (NCBI) False
RSP_4337 RSP_4337 tRNA None chromosome 2 923865 923940 - tRNA-Val (NCBI) False
RSP_4338 RSP_4338 tRNA None chromosome 1 479857 479943 + tRNA-Leu (NCBI) False
RSP_4339 RSP_4339 tRNA None chromosome 2 431027 431102 + tRNA-Ala (NCBI) False
RSP_4340 RSP_4340 tRNA None chromosome 1 857015 857098 - tRNA-Tyr (NCBI) 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.

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.