Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 127 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 127

There are 14 regulatory influences for Module 127

Regulator Table (14)
Regulator Name Type
RSP_2610 tf
RSP_1550 tf
RSP_2425 tf
RSP_0316 tf
RSP_1606 tf
RSP_0698 tf
RSP_1871 tf
RSP_0402 tf
RSP_2591 tf
RSP_0415 tf
RSP_0087 tf
RSP_0755 tf
RSP_3124 tf
RSP_1890 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
7974 6.10e+02 ATatTTGc.CagAGtGaAaGCG
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7975 4.30e+03 tTTTTCA
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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 127 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 2.93e-02 4.46e-02 7/31
Cell wall/membrane/envelope biogenesis cog subcategory 2.90e-02 4.41e-02 3/31
Amino acid transport and metabolism cog subcategory 2.03e-02 3.15e-02 6/31
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 127

There are 31 genes in Module 127

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0359 cbbI CDS None chromosome 1 2090051 2090839 - Ribose-5-phosphate isomerase (NCBI) False
RSP_0683 RSP_0683 CDS None chromosome 1 2427172 2427585 + hypothetical protein (NCBI) False
RSP_0758 RSP_0758 CDS None chromosome 1 2501050 2501646 - Lumazine-binding protein (NCBI) False
RSP_0762 RSP_0762 CDS None chromosome 1 2504287 2504685 - transcriptional regulator, XRE family (NCBI) False
RSP_0999 RSP_0999 CDS None chromosome 1 2757701 2758255 - hypothetical protein (NCBI) True
RSP_1001 RSP_1001 CDS None chromosome 1 2759368 2760150 - hypothetical protein (NCBI) False
RSP_1007 RSP_1007 CDS None chromosome 1 2765413 2766186 - hypothetical protein (NCBI) False
RSP_1029 RSP_1029 CDS None chromosome 1 2793413 2793808 - possible Histidine triad (HIT) protein (NCBI) False
RSP_1126 rnr CDS None chromosome 1 2889366 2891624 - Exoribonuclease R (NCBI) False
RSP_1385 RSP_1385 CDS None chromosome 1 3163866 3164705 - hypothetical protein (NCBI) False
RSP_1430 RSP_1430 CDS None chromosome 1 9690 11195 + hypothetical protein (NCBI) False
RSP_1550 RSP_1550 CDS None chromosome 1 141230 142060 - regulatory proteins, IclR family (NCBI) True
RSP_1868 RSP_1868 CDS None chromosome 1 465545 466672 + serine-pyruvate aminotransferase (NCBI) False
RSP_2120 RSP_2120 CDS None chromosome 1 720796 722169 - putative D-lactate dehydrogenase (cytochrome), FAD/FMN-containing oxidoreductase (NCBI) False
RSP_2139 RSP_2139 CDS None chromosome 1 739608 740066 - hypothetical protein (NCBI) False
RSP_2173 RSP_2173 CDS None chromosome 1 777316 777861 - hypothetical protein (NCBI) False
RSP_2174 RSP_2174 CDS None chromosome 1 777875 778465 - Putative ABC transporter, inner membrane subunit (NCBI) False
RSP_2216 ilvE CDS None chromosome 1 828137 829000 - Aminotransferase, class IV (NCBI) False
RSP_2309 RSP_2309 CDS None chromosome 1 931046 932101 - hypothetical protein (NCBI) False
RSP_2399 RSP_2399 CDS None chromosome 1 1026870 1027763 - ABC putrescine transporter, inner membrane subunit (NCBI) False
RSP_2400 RSP_2400 CDS None chromosome 1 1027765 1028769 - ABC putrescine transporter, ATPase subunit (NCBI) False
RSP_2401 RSP_2401 CDS None chromosome 1 1028860 1030317 - putative 6-aminohexanoate-cyclic-dimer hydrolase (NCBI) False
RSP_2610 RSP_2610 CDS None chromosome 1 1251470 1252315 - trancriptional regulator, MerR family (NCBI) True
RSP_2611 ihfA CDS None chromosome 1 1252322 1252624 - Histone-like DNA-binding protein (IHF) (NCBI) False
RSP_2772 ftsJ CDS None chromosome 1 1419622 1420356 + 23S rRNA methylase (NCBI) False
RSP_2775 lpxD CDS None chromosome 1 1423051 1424142 + UDP-3-O-(3-hydroxymyristoyl) glucosamine N-acyltransferase (NCBI) False
RSP_2862 RSP_2862 CDS None chromosome 1 1437761 1438945 - Glycine/D-amino acid oxidases (deaminating) (NCBI) False
RSP_2900 RSP_2900 CDS None chromosome 1 1575712 1576842 + Predicted permease (NCBI) False
RSP_2947 RSP_2947 CDS None chromosome 1 1627146 1627958 - Glutamate racemase (NCBI) False
RSP_2969 RSP_2969 CDS None chromosome 1 1653920 1654495 - hypothetical protein (NCBI) False
RSP_3563 RSP_3563 CDS None chromosome 2 658350 659456 + putative FAD-dependent glycerol-3-phosphate dehydrogenase 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.

Comments for Module 127

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.