Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 372 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 372

There are 14 regulatory influences for Module 372

Regulator Table (14)
Regulator Name Type
RSP_1776 tf
RSP_0611 tf
RSP_0774 tf
RSP_1663 tf
RSP_1225 tf
RSP_2533 tf
RSP_2606 tf
RSP_2494 tf
RSP_1590 tf
RSP_3179 tf
RSP_0122 tf
RSP_0386 tf
RSP_0601 tf
RSP_0755 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
8438 1.40e-05 CCTTgttcTttgcggcCgccttt
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8439 1.60e+03 aAGcagCagaac.aT.tcGGT
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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 372 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Genetic Information Processing kegg category 1.04e-02 2.69e-02 5/30
Replication and Repair kegg subcategory 5.85e-04 4.30e-03 3/30

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
DNA metabolism tigr mainrole 1.05e-04 2.12e-04 4/30
DNA replication, recombination, and repair tigr sub1role 6.50e-05 1.35e-04 4/30

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 7.71e-03 1.26e-02 8/30
Poorly characterized cog category 2.37e-02 3.66e-02 9/30
Replication, recombination and repair cog subcategory 1.79e-03 3.12e-03 4/30
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 372

There are 30 genes in Module 372

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0193 RSP_0193 CDS None chromosome 1 1909873 1910244 - hypothetical protein (NCBI) False
RSP_0195 RSP_0195 CDS None chromosome 1 1910711 1911085 - NADH-ubiquinone oxidoreductase 17.2 kD subunit (NCBI) False
RSP_0247 RSP_0247 CDS None chromosome 1 1971361 1972128 + aminomethyltransferase related to GcvT (NCBI) False
RSP_0359 cbbI CDS None chromosome 1 2090051 2090839 - Ribose-5-phosphate isomerase (NCBI) False
RSP_0553 ruvB CDS None chromosome 1 2290834 2291859 - Holiday junction DNA helicase RuvB (NCBI) False
RSP_0882 DapA CDS None chromosome 1 2632363 2633250 + Dihydrodipicolinate synthetase (NCBI) False
RSP_1200 RSP_1200 CDS None chromosome 1 2970334 2970888 + putative membrane protein (NCBI) False
RSP_1343 RSP_1343 CDS None chromosome 1 3112260 3113378 + DNA polymerase III, beta chain (NCBI) False
RSP_1346 RSP_1346 CDS None chromosome 1 3115048 3117483 + DNA gyrase, subunit B (NCBI) False
RSP_1490 RSP_1490 CDS None chromosome 1 75342 76010 + Putative ATP-dependent protease La, LON (NCBI) False
RSP_1511 RSP_1511 CDS None chromosome 1 98604 98876 + hypothetical protein (NCBI) False
RSP_1562 RSP_1562 CDS None chromosome 1 152005 152691 - fumarylacetoacetate hydrolase family protein (NCBI) False
RSP_1776 greA CDS None chromosome 1 360057 360527 - Transcription elongation factor greA (NCBI) True
RSP_1833 RSP_1833 CDS None chromosome 1 425150 425734 + putative ribosomal-protein-alanine acetyltransferase (NCBI) False
RSP_1875 RSP_1875 CDS None chromosome 1 473997 474455 + hypothetical protein (NCBI) False
RSP_1947 cbbJ CDS None chromosome 1 545193 545930 - Triosephosphate isomerase (NCBI) False
RSP_1969 purM CDS None chromosome 1 560737 561783 + Phosphoribosylformylglycinamidine cyclo-ligase (NCBI) False
RSP_2009 argF CDS None chromosome 1 610890 611816 + Aspartate/ornithine carbamoyltransferase (NCBI) False
RSP_2038 RSP_2038 CDS None chromosome 1 633935 634387 + possible acetyltransferase (NCBI) False
RSP_2082 RSP_2082 CDS None chromosome 1 676328 676639 - putative NADH-ubiquinone oxidoreductase-related protein (NCBI) False
RSP_2083 uvrB CDS None chromosome 1 676895 679078 + Putative Excinuclease subunit B (NCBI) False
RSP_2519 RSP_2519 CDS None chromosome 1 1163417 1163776 + hypothetical protein (NCBI) False
RSP_2533 RSP_2533 CDS None chromosome 1 1175279 1176052 + Putative transcriptional regulator (NCBI) True
RSP_2542 RSP_2542 CDS None chromosome 1 1185748 1186587 + ATPase (NCBI) False
RSP_2647 RSP_2647 CDS None chromosome 1 1290283 1291473 + Predicted SAM-dependent methyltransferases (NCBI) False
RSP_2943 argS CDS None chromosome 1 1622549 1624300 - Arginyl-tRNA synthetase, class I (NCBI) False
RSP_2976 RSP_2976 CDS None chromosome 1 1663458 1664234 - hypothetical protein (NCBI) False
RSP_3261 bioA CDS None chromosome 2 318320 319702 + Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (BioA) (NCBI) False
RSP_3262 RSP_3262 CDS None chromosome 2 319706 320137 + Putative thioesterase (NCBI) False
RSP_4315 RSP_4315 tRNA None chromosome 1 560555 560630 - tRNA-Met (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 372

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.