Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 271 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 271

There are 15 regulatory influences for Module 271

Regulator Table (15)
Regulator Name Type
RSP_3238 tf
RSP_0547 tf
RSP_2494 tf
RSP_0386 tf
RSP_2130 tf
RSP_0623 tf
RSP_1092 tf
RSP_1776 tf
RSP_1231 tf
RSP_1739 tf
RSP_3317 tf
RSP_2027 tf
RSP_0999 tf
RSP_1225 tf
RSP_0443 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
8258 9.70e-04 CacAAgCCgaaGgat.TgC
Loader icon
8259 4.50e+00 GGGaaGaAGCGGacAaAcGT
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 271 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 8.35e-03 2.30e-02 10/25
Nucleotide Metabolism kegg subcategory 2.98e-03 1.21e-02 3/25
Amino Acid Metabolism kegg subcategory 2.91e-03 1.19e-02 5/25
Global kegg category 8.04e-03 2.25e-02 9/25
Metabolism kegg subcategory 8.04e-03 2.25e-02 9/25
Metabolic pathways kegg pathway 1.67e-02 3.70e-02 8/25
Microbial metabolism in diverse environments kegg pathway 3.06e-04 2.72e-03 6/25

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 4.73e-03 6.57e-03 3/25
Unknown function tigr mainrole 5.32e-04 9.42e-04 3/25

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 7.76e-03 1.27e-02 7/25
Translation, ribosomal structure and biogenesis cog subcategory 5.30e-05 1.41e-04 6/25
Amino acid transport and metabolism cog subcategory 2.32e-02 3.58e-02 5/25
Acetyltransferases, including N-acetylases of ribosomal proteins cog 0.00e+00 0.00e+00 3/25
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 271

There are 25 genes in Module 271

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0448 RSP_0448 CDS None chromosome 1 2178615 2180435 + EF-Tu; elongation factor Tu (NCBI) False
RSP_0490 RSP_0490 CDS None chromosome 1 2223935 2224687 + carbohydrate kinase (NCBI) False
RSP_0705 RSP_0705 CDS None chromosome 1 2450768 2451292 - Cytochrome cy (NCBI) False
RSP_0706 pheA CDS None chromosome 1 2451344 2452246 + Prephenate dehydratase (NCBI) False
RSP_0901 RSP_0901 CDS None chromosome 1 2651080 2651634 + N-6 Adenine-specific DNA methylase (NCBI) False
RSP_0902 RSP_0902 CDS None chromosome 1 2651631 2652275 + Hydrolase, haloacid dehalogenase-like hydrolase (NCBI) False
RSP_1050 RSP_1050 CDS None chromosome 1 2808511 2809071 - Acetyltransferase (GNAT) family (NCBI) False
RSP_1051 RSP_1051 CDS None chromosome 1 2809068 2809598 - hypothetical protein (NCBI) False
RSP_1052 RSP_1052 CDS None chromosome 1 2809595 2810131 - possible Acetyltransferase (NCBI) False
RSP_1110 RSP_1110 CDS None chromosome 1 2867723 2868235 + hypothetical protein (NCBI) False
RSP_1132 RSP_1132 CDS None chromosome 1 2895372 2896196 + hypothetical protein (NCBI) False
RSP_1146 gltB CDS None chromosome 1 2906721 2911259 - Glutamine-pyruvate aminotransferase (NCBI) False
RSP_1474 nspC CDS None chromosome 1 58616 59713 + putative carboxynorspermidine decarboxylase protein (NCBI) False
RSP_1475 RSP_1475 CDS None chromosome 1 59750 60988 + saccharopine dehydrogenase family (NCBI) False
RSP_1575 sopT CDS None chromosome 1 166955 168718 - sulfate adenylyltransferase (NCBI) False
RSP_1849 RSP_1849 CDS None chromosome 1 441351 442610 + Aspartate kinase (NCBI) False
RSP_2303 RSP_2303 CDS None chromosome 1 926578 927039 - hypothetical protein (NCBI) False
RSP_2699 RSP_2699 CDS None chromosome 1 1345615 1347078 + Probable GTP-binding protein (NCBI) False
RSP_2739 RSP_2739 CDS None chromosome 1 1388804 1389931 + hypothetical protein (NCBI) False
RSP_2977 prfB CDS None chromosome 1 1664604 1665731 - Peptide chain release factor 2 (NCBI) False
RSP_3547 RSP_3547 CDS None chromosome 2 636449 638716 - Ribonucleotide reductase (NCBI) False
RSP_3548 RSP_3548 CDS None chromosome 2 638868 639299 + hypothetical protein (NCBI) False
RSP_3591 RSP_3591 CDS None chromosome 2 683499 684119 - cytidylate kinase (NCBI) False
RSP_3600 miaB CDS None chromosome 2 692968 694278 - MiaB tRNA modification protein (Radical SAM) (NCBI) False
RSP_3829 RSP_3829 CDS None chromosome 2 24699 25430 + tRNA/rRNA methyltransferase (SpoU) (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.

Comments for Module 271

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.