Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 93 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 93

There are 7 regulatory influences for Module 93

Regulator Table (7)
Regulator Name Type
RSP_2494 tf
RSP_1231 tf
RSP_0087 tf
RSP_0395 tf
RSP_2922 tf
RSP_2171 tf
RSP_1590 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
7906 6.90e-11 tgtcaaTgcCTTTCcGActc
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7907 6.70e-07 aaAAaccCcgAAAaTCacGgca
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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 93 is enriched for following functions.

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 93

There are 29 genes in Module 93

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0002 spbB CDS None chromosome 1 1704125 1704520 - Histone-like nucleoid-structuring protein H-NS (NCBI) False
RSP_0146 glnB CDS None chromosome 1 1859643 1859981 + Nitrogen regulatory protein P-II (NCBI) False
RSP_0147 glnA CDS None chromosome 1 1860063 1861472 + Glutamine synthetase class-I (NCBI) False
RSP_0223 RSP_0223 CDS None chromosome 1 1938711 1939982 + hypothetical protein (NCBI) False
RSP_0224 RSP_0224 CDS None chromosome 1 1939988 1942159 + ATP-dependent helicase (NCBI) False
RSP_0452 recA CDS None chromosome 1 2184461 2185534 - Recombinase A, DNA recombination protein (NCBI) False
RSP_0797 gltX-1 CDS None chromosome 1 2541066 2542391 - Glutamyl-tRNA synthetase, class Ic (NCBI) False
RSP_0831 trpA CDS None chromosome 1 2576608 2577399 - Tryptophan synthase, alpha chain (NCBI) False
RSP_0981 RSP_0981 CDS None chromosome 1 2739750 2740436 - Transcriptional regulator, GntR family (NCBI) True
RSP_0982 RSP_0982 CDS None chromosome 1 2740433 2741119 - zinc metallopeptidases-like protein (NCBI) False
RSP_0983 RSP_0983 CDS None chromosome 1 2741231 2741611 + hypothetical protein (NCBI) False
RSP_1085 RSP_1085 CDS None chromosome 1 2843493 2843738 + hypothetical protein (NCBI) False
RSP_1360 RSP_1360 CDS None chromosome 1 3139224 3139529 - hypothetical protein (NCBI) False
RSP_1459 RSP_1459 CDS None chromosome 1 45667 46413 + hypothetical protein (NCBI) False
RSP_1460 RSP_1460 CDS None chromosome 1 46555 46800 + hypothetical protein (NCBI) False
RSP_1621 RSP_1621 CDS None chromosome 1 217914 219383 + Deoxyguanosinetriphosphate triphosphohydrolase-like protein (NCBI) False
RSP_1622 RSP_1622 CDS None chromosome 1 220172 221230 - Putative DNA-binding protein (NCBI) False
RSP_1623 RSP_1623 CDS None chromosome 1 219377 220213 + hypothetical protein (NCBI) False
RSP_1977 cobS CDS None chromosome 1 569466 570560 - cobalt chelatase, CobS small subunit (NCBI) False
RSP_1978 RSP_1978 CDS None chromosome 1 570606 571241 - molecular chaperone, DnaJ family (NCBI) False
RSP_1979 RSP_1979 CDS None chromosome 1 571316 571573 + stress induced morphogen, BolA (NCBI) False
RSP_1997 lexA CDS None chromosome 1 596014 596700 - LexA repressor (NCBI) False
RSP_2246 hisB CDS None chromosome 1 862146 862733 - Imidazoleglycerol-phosphate dehydratase (NCBI) False
RSP_2329 mreB CDS None chromosome 1 952681 953718 - Cell shape determining protein MreB/Mrl (NCBI) False
RSP_2356 RSP_2356 CDS None chromosome 1 981816 983288 + hypothetical protein (NCBI) False
RSP_2361 RSP_2361 CDS None chromosome 1 987339 989156 - putative integrase/resolvase recombinase protein phage-related integrase (NCBI) False
RSP_2624 RSP_2624 CDS None chromosome 1 1264784 1264906 + hypothetical protein (NCBI) False
RSP_3003 RSP_3003 CDS None chromosome 2 39397 39693 + hypothetical protein (NCBI) False
RSP_3644 RSP_3644 CDS None chromosome 2 751763 753184 - Metal dependent phosphohydrolase (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 93

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.