Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 5 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 5

There are 17 regulatory influences for Module 5

Regulator Table (17)
Regulator Name Type
RSP_2838 tf
RSP_0623 tf
RSP_1739 tf
RSP_0415 tf
RSP_2130 tf
RSP_1164 tf
RSP_3665 tf
RSP_1225 tf
RSP_1055 tf
RSP_1892 tf
RSP_1435 tf
RSP_2965 tf
RSP_0395 tf
RSP_1776 tf
RSP_2853 tf
RSP_0386 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
7732 4.20e+00 cGcct.gattTTtC.
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7733 1.30e+04 TcCcggcccacgGgCGGaagaac
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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 5 is enriched for following functions.

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
Cell envelope tigr mainrole 4.40e-05 9.70e-05 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 4.65e-04 9.15e-04 5/25
Cell wall/membrane/envelope biogenesis cog subcategory 1.39e-02 2.21e-02 3/25
Inorganic ion transport and metabolism cog subcategory 8.65e-04 1.59e-03 5/25
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 5

There are 25 genes in Module 5

Gene Member Table (25)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0129 metN CDS None chromosome 1 1844020 1845081 + ABC D-methionine uptake transporter, ATPase subunit (NCBI) False
RSP_0130 metI CDS None chromosome 1 1845071 1845745 + ABC D-methionine uptake transporter, inner membrane subunit (NCBI) False
RSP_0132 metQ CDS None chromosome 1 1845774 1846550 + ABC D-methionine uptake transporter, substrate-binding protein (NCBI) False
RSP_0356 RSP_0356 CDS None chromosome 1 2086429 2087451 - Probable HflC protein (NCBI) False
RSP_0840 leuS CDS None chromosome 1 2588362 2590905 - LeuS, leucyl-tRNA synthetase (NCBI) False
RSP_1047 rimM CDS None chromosome 1 2807173 2807682 - putative 16S rRNA processing protein (NCBI) False
RSP_1048 rpsP CDS None chromosome 1 2807783 2808133 - 30S ribosomal protein S16 (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_1066 RSP_1066 CDS None chromosome 1 2823936 2824589 + Probable GTP-binding protein (NCBI) False
RSP_1940 RSP_1940 CDS None chromosome 1 538996 539403 - hypothetical protein (NCBI) False
RSP_1941 cysH CDS None chromosome 1 539400 540116 - Phosphoadenosine phosphosulfate reductase (NCBI) False
RSP_1942 RSP_1942 CDS None chromosome 1 540145 541815 - Sulfite/nitrite reductase hemoprotein subunit (NCBI) False
RSP_2108 murC CDS None chromosome 1 708980 710392 + UDP-N-acetylmuramate-alanine ligase (NCBI) False
RSP_2109 RSP_2109 CDS None chromosome 1 710406 710660 + hypothetical protein (NCBI) False
RSP_2110 murB CDS None chromosome 1 710657 711583 + UDP-N-acetylenolpyruvoylglucosamine reductase/dehydrogenase (NCBI) False
RSP_2113 ftsA CDS None chromosome 1 713457 714791 + cell division protein FtsA (NCBI) False
RSP_2156 RSP_2156 CDS None chromosome 1 759416 760213 - ABC transporter, inner membrane subunit (NCBI) False
RSP_2178 topA CDS None chromosome 1 782378 785032 + DNA topoisomerase I (NCBI) False
RSP_2568 sqdD CDS None chromosome 1 1212607 1213389 - glycosyl transferase (sulfolipid biosynthesis) protein (NCBI) False
RSP_2684 RSP_2684 CDS None chromosome 1 1329031 1329513 - putative endonuclease involved in recombination (NCBI) False
RSP_2738 RSP_2738 CDS None chromosome 1 1387846 1388793 + Probable Rhodanese-related sulfurtransferase (NCBI) False
RSP_2739 RSP_2739 CDS None chromosome 1 1388804 1389931 + hypothetical protein (NCBI) False
RSP_3719 RSP_3719 CDS None chromosome 2 842210 843724 + Polysaccharide export transporter, PST Family (NCBI) False
RSP_3720 RSP_3720 CDS None chromosome 2 843736 844689 + hypothetical protein (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.