Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 107 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 107

There are 14 regulatory influences for Module 107

Regulator Table (14)
Regulator Name Type
RSP_3309 tf
RSP_1712 tf
RSP_0032 tf
RSP_0395 tf
RSP_1606 tf
RSP_1550 tf
RSP_1032 tf
RSP_0327 tf
RSP_0122 tf
RSP_0755 tf
RSP_3022 tf
RSP_0394 tf
RSP_0591 tf
RSP_2165 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
7934 5.30e+00 cCAGAaGCaGa
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7935 1.70e+02 AggATggggGC
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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 107 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 1.91e-03 9.24e-03 6/31
Histidine metabolism kegg pathway 2.30e-05 3.60e-04 3/31
Biosynthesis of secondary metabolites kegg pathway 4.47e-03 1.55e-02 6/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 3.21e-02 4.85e-02 15/31
Coenzyme transport and metabolism cog subcategory 3.02e-02 4.60e-02 3/31
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 107

There are 31 genes in Module 107

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0148 RSP_0148 CDS None chromosome 1 1861665 1862717 - Signal transduction histidine kinase (NCBI) False
RSP_0149 RSP_0149 CDS None chromosome 1 1862714 1863151 - CheY-like receiver protein (NCBI) False
RSP_0153 RSP_0153 CDS None chromosome 1 1867577 1868254 - hypothetical protein (NCBI) False
RSP_0198 RSP_0198 CDS None chromosome 1 1913399 1914007 - Phosphatidylglycerophosphate synthase (NCBI) False
RSP_0365 RSP_0365 CDS None chromosome 1 2094867 2095748 - hypothetical protein (NCBI) False
RSP_0388 RSP_0388 CDS None chromosome 1 2120180 2120584 - hypothetical protein (NCBI) False
RSP_0392 RSP_0392 CDS None chromosome 1 2122280 2122708 + probable lactoylglutathione lyase (NCBI) False
RSP_0393 RSP_0393 CDS None chromosome 1 2122870 2123940 - probable riboflavin biosynthesis protein (NCBI) False
RSP_0552 RSP_0552 CDS None chromosome 1 2290223 2290564 + putative multidrug transporter, SMR family, DMT Superfamily (NCBI) False
RSP_0795 RSP_0795 CDS None chromosome 1 2538620 2539039 - hypothetical protein (NCBI) False
RSP_0865 RSP_0865 CDS None chromosome 1 2616422 2616742 + hypothetical protein (NCBI) False
RSP_0935 RSP_0935 CDS None chromosome 1 2685220 2686497 - MiaB-like Radical SAM protein (NCBI) False
RSP_1032 RSP_1032 CDS None chromosome 1 2796013 2796861 + possible O6-methylguanine-DNA methyltransferase (NCBI) True
RSP_1234 aroE CDS None chromosome 1 3005859 3006698 + putative shikimate 5-dehydrogenase (NCBI) False
RSP_1292 RSP_1292 CDS None chromosome 1 3059735 3061219 - putative Aldehyde dehydrogenase (NCBI) False
RSP_1558 RSP_1558 CDS None chromosome 1 148997 150340 - putative 2-dehydropantoate 2-reductase (NCBI) False
RSP_1965 RSP_1965 CDS None chromosome 1 556550 557740 + Putative Membrane Fusion Protein Family member (NCBI) False
RSP_1971 rnd CDS None chromosome 1 562467 563624 + Ribonuclease D (NCBI) False
RSP_1984 RSP_1984 CDS None chromosome 1 579524 580669 + histidinol-phosphate-aminotransferase (NCBI) False
RSP_2127 purS CDS None chromosome 1 727669 727908 + Component of phosphoribosylformylglycinamidine (FGAM) synthetase (NCBI) False
RSP_2165 putR CDS None chromosome 1 767169 767624 - transcriptional regulator, AsnC family (NCBI) True
RSP_2241 hisI CDS None chromosome 1 858840 859151 - Phosphoribosyl-ATP pyrophosphohydrolase (NCBI) False
RSP_2282 chrA CDS None chromosome 1 903198 904376 - Chromate efflux pump, ChrA (NCBI) False
RSP_2287 RSP_2287 CDS None chromosome 1 909607 910155 + ChaC-like protein (NCBI) False
RSP_2411 RSP_2411 CDS None chromosome 1 1040755 1041555 - hypothetical protein (NCBI) False
RSP_2642 RSP_2642 CDS None chromosome 1 1283010 1283480 - hypothetical protein (NCBI) False
RSP_2903 RSP_2903 CDS None chromosome 1 1580094 1581401 + Probable PpiC-type peptidyl-prolyl cis-trans isomerase (NCBI) False
RSP_3071 RSP_3071 CDS None chromosome 2 110019 111290 + putative hydroxypyruvate reductase/glycerate kinase (NCBI) False
RSP_3309 RSP_3309 CDS None chromosome 2 369832 370551 - transcriptional regulator, AraC family (NCBI) True
RSP_3350 RSP_3350 CDS None chromosome 2 416189 417142 + Lipocalin-related protein (NCBI) False
RSP_3695 argE CDS None chromosome 2 815720 816814 - putative acetylornithine deacetylase (acetylornithinase) (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 107

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.