Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 381 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 381

There are 18 regulatory influences for Module 381

Regulator Table (18)
Regulator Name Type
RSP_2882 tf
RSP_0415 tf
RSP_2838 tf
RSP_1663 tf
RSP_1034 tf
RSP_1243 tf
RSP_2922 tf
RSP_1297 tf
RSP_3226 tf
RSP_0402 tf
RSP_2840 tf
RSP_2171 tf
RSP_1590 tf
RSP_3202 tf
RSP_1550 tf
RSP_0090 tf
RSP_2591 tf
RSP_0087 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
8452 3.00e-01 gtCgGGccGCgGcggCggC.at
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8453 3.30e+00 CatcGGaggcTCCttctTcC
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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 381 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 9.47e-03 2.50e-02 12/32
Nucleotide Metabolism kegg subcategory 1.05e-04 1.24e-03 5/32
Purine metabolism kegg pathway 2.39e-04 2.30e-03 4/32
Pyrimidine metabolism kegg pathway 5.50e-04 4.12e-03 3/32

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Purines, pyrimidines, nucleosides, and nucleotides tigr mainrole 5.96e-04 1.04e-03 3/32
DNA metabolism tigr mainrole 1.67e-03 2.62e-03 3/32
DNA replication, recombination, and repair tigr sub1role 1.15e-03 1.89e-03 3/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 1.21e-02 1.94e-02 8/32
Transcription cog subcategory 2.37e-02 3.65e-02 4/32
Replication, recombination and repair cog subcategory 2.41e-03 4.12e-03 4/32
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 381

There are 32 genes in Module 381

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0282 ppsR CDS None chromosome 1 2007910 2009304 - Transcriptional regulator, PpsR (NCBI) True
RSP_0384 RSP_0384 CDS None chromosome 1 2116163 2116927 - hypothetical protein (NCBI) False
RSP_0415 RSP_0415 CDS None chromosome 1 2150594 2151187 - sigma-24 (NCBI) True
RSP_0599 RSP_0599 CDS None chromosome 1 2340411 2341601 - Probable DNA/pantothenate metabolism flavoprotein (NCBI) False
RSP_0708 RSP_0708 CDS None chromosome 1 2452809 2453762 - NUDIX hydrolase (NCBI) False
RSP_0710 dnaX CDS None chromosome 1 2456212 2457960 + DNA polymerase III tau and gamma subunits (NCBI) False
RSP_1188 wcaG CDS None chromosome 1 2961261 2963147 - Nucleotide sugar epimerase/dehydratase (NCBI) False
RSP_1214 RSP_1214 CDS None chromosome 1 2984836 2985558 - putative branched-chain amino acid aminotransferase (NCBI) False
RSP_1215 ilvE CDS None chromosome 1 2985555 2986454 - putative IlvE, Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase (NCBI) False
RSP_1342 dnaA CDS None chromosome 1 3110775 3112142 + chromosomal replication initiator protein, DnaA (NCBI) False
RSP_1404 RSP_1404 CDS None chromosome 1 3181030 3181797 - Orotidine 5'-phosphate decarboxylase (NCBI) False
RSP_1405 RSP_1405 CDS None chromosome 1 3181832 3182719 + ROK family protein (NCBI) False
RSP_1520 prrB CDS None chromosome 1 105908 107296 + Sensor histidine kinase PrrB (RegB) (NCBI) False
RSP_1553 RSP_1553 CDS None chromosome 1 143434 144270 - Probable glyoxylate induced protein (NCBI) False
RSP_1554 RSP_1554 CDS None chromosome 1 144267 145682 - Possible polysaccharide deacetylase (NCBI) False
RSP_1555 RSP_1555 CDS None chromosome 1 145829 146182 + Transthyretin-like protein (NCBI) False
RSP_1566 RSP_1566 CDS None chromosome 1 156951 157640 + hypothetical protein (NCBI) False
RSP_1621 RSP_1621 CDS None chromosome 1 217914 219383 + Deoxyguanosinetriphosphate triphosphohydrolase-like protein (NCBI) False
RSP_1894 RSP_1894 CDS None chromosome 1 490925 491314 + hypothetical protein (NCBI) False
RSP_1908 RSP_1908 CDS None chromosome 1 505718 506359 - outer membrane protein, OmpA/MotB family (NCBI) False
RSP_1909 RSP_1909 CDS None chromosome 1 506365 507750 - Outer membrane general secretion pathway protein, Secretin (NCBI) False
RSP_1946 RSP_1946 CDS None chromosome 1 543683 544864 - Cytochrome P450 hydroxylase (NCBI) False
RSP_2119 RSP_2119 CDS None chromosome 1 720407 720799 - hypothetical protein (NCBI) False
RSP_2694 RSP_2694 CDS None chromosome 1 1339516 1340070 - hypothetical protein (NCBI) False
RSP_2869 RSP_2869 CDS None chromosome 1 1536836 1537810 - Possible tellurite resistance protein (NCBI) False
RSP_2882 RSP_2882 CDS None chromosome 1 1553749 1554429 - two component transcriptional regulator, LuxR family (NCBI) True
RSP_2942 RSP_2942 CDS None chromosome 1 1621492 1622478 - hypothetical protein (NCBI) False
RSP_3226 RSP_3226 CDS None chromosome 2 285189 285881 + Silent information regulator protein, Sir2 (NCBI) True
RSP_3376 aroQ CDS None chromosome 2 441010 441453 - 3 dehydroquinase dehydratase, class II (NCBI) False
RSP_3419 RSP_3419 CDS None chromosome 2 487758 488336 + hypothetical protein (NCBI) False
RSP_3507 RSP_3507 CDS None chromosome 2 586352 586660 + hypothetical protein (NCBI) False
RSP_3553 dnaE CDS None chromosome 2 643014 646505 - DNA polymerase III alpha chain (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 381

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.