Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 64 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 64

There are 10 regulatory influences for Module 64

Regulator Table (10)
Regulator Name Type
RSP_3238 tf
RSP_2200 tf
RSP_2801 tf
RSP_0794 tf
RSP_2610 tf
RSP_0316 tf
RSP_1139 tf
RSP_2425 tf
RSP_3694 tf
RSP_0122 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
7848 3.00e-05 TtttTGaCTtT
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7849 1.20e-03 CG.gCAga.gGtt.cgtAaAcGAC
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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 64 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Environmental Information Processing kegg category 5.49e-03 1.76e-02 6/28
Membrane Transport kegg subcategory 3.73e-03 1.38e-02 5/28
ABC transporters kegg pathway 1.99e-03 9.49e-03 5/28
Microbial metabolism in diverse environments kegg pathway 1.76e-02 3.83e-02 4/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 3.34e-03 5.64e-03 16/28
Energy production and conversion cog subcategory 4.78e-03 7.97e-03 5/28
Carbohydrate transport and metabolism cog subcategory 3.64e-03 6.13e-03 5/28
Lipid transport and metabolism cog subcategory 1.36e-02 2.17e-02 3/28
Function unknown cog subcategory 1.76e-02 2.76e-02 5/28
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 64

There are 28 genes in Module 64

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0091 smoE CDS None chromosome 1 1801150 1802460 + ABC sorbitol/mannitol transporter, periplasmic binding protein (NCBI) False
RSP_0092 smoF CDS None chromosome 1 1802562 1803434 + ABC sorbitol/mannitol transporter, inner membrane subunit (NCBI) False
RSP_0093 smoG CDS None chromosome 1 1803436 1804266 + ABC sorbitol/mannitol transporter, inner membrane subunit (NCBI) False
RSP_0094 smoK CDS None chromosome 1 1804274 1805272 + ABC sorbitol/mannitol transporter, ATPase subunit (NCBI) False
RSP_0095 smoS CDS None chromosome 1 1805274 1806044 + Sorbitol dehydrogenase (NCBI) False
RSP_0096 mtlK CDS None chromosome 1 1806098 1807531 + Mannitol dehydrogenase (NCBI) False
RSP_0458 RSP_0458 CDS None chromosome 1 2191438 2191854 - hypothetical protein (NCBI) False
RSP_1138 RSP_1138 CDS None chromosome 1 2900890 2901588 - two component transcriptional regulator, winged helix family (NCBI) False
RSP_1139 RSP_1139 CDS None chromosome 1 2901585 2902094 - transcriptional regulator, MarR family (NCBI) True
RSP_1140 ilvE CDS None chromosome 1 2902250 2903116 + Branched chain acid aminotransferase (NCBI) False
RSP_1679 RSP_1679 CDS None chromosome 1 268195 269841 - acyl-CoA dehydrogenase (NCBI) False
RSP_1880 RSP_1880 CDS None chromosome 1 478176 479735 + hypothetical protein (NCBI) False
RSP_2007 RSP_2007 CDS None chromosome 1 608386 609009 - conservd hypothetical protein (NCBI) False
RSP_2261 ydjI CDS None chromosome 1 878349 879458 - Antifreeze protein, type I (NCBI) False
RSP_2481 cysE CDS None chromosome 1 1120739 1121545 + serine acetyltransferase (NCBI) False
RSP_2590 RSP_2590 CDS None chromosome 1 1232486 1233292 + hypothetical protein (NCBI) False
RSP_2763 RSP_2763 CDS None chromosome 1 1410065 1410313 + hypothetical protein (NCBI) False
RSP_2801 tetR CDS None chromosome 1 1518439 1519008 + transcriptional regulator, TetR family, (NCBI) True
RSP_2802 RSP_2802 CDS None chromosome 1 1517118 1518293 - multidrug/cation efflux pump, membrane fusion protein subunit (NCBI) False
RSP_2803 RSP_2803 CDS None chromosome 1 1514033 1517110 - multidrug/cation efflux pump, RND superfamily (NCBI) False
RSP_2856 RSP_2856 CDS None chromosome 1 1444233 1446044 + putative oligopeptide ABC transporter, periplasmic-binding protein (NCBI) False
RSP_2876 RSP_2876 CDS None chromosome 1 1545836 1546621 - putative carbon monoxide dehydrogenase medium chain (NCBI) False
RSP_2877 coxL CDS None chromosome 1 1546632 1549004 - Putative carbon monoxide dehydrogenase large chain (NCBI) False
RSP_2878 coxS CDS None chromosome 1 1549033 1549515 - Putative carbon-monoxide dehydrogenase small chain (NCBI) False
RSP_2879 RSP_2879 CDS None chromosome 1 1549544 1550074 - hypothetical protein (NCBI) False
RSP_2948 RSP_2948 CDS None chromosome 1 1628096 1631482 - Putative Pyruvate ferredoxin/flavodoxin oxidoreductase (NCBI) False
RSP_2982 gcpE CDS None chromosome 1 1672163 1673296 - Probable 4-hydroxy-3-methylbut-2-en-1-yl diphosphate (NCBI) False
RSP_3562 sqr CDS None chromosome 2 657065 658345 + sulfide-quinone reductase (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 64

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.