Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 238 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 238

There are 11 regulatory influences for Module 238

Regulator Table (11)
Regulator Name Type
RSP_1077 tf
RSP_1055 tf
RSP_2867 tf
RSP_2610 tf
RSP_2681 tf
RSP_3684 tf
RSP_1776 tf
RSP_3464 tf
RSP_1014 tf
RSP_1231 tf
RSP_3322 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
8194 9.90e+03 TATTTTA
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8195 3.90e+04 atCAtTttAAtCa
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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 238 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 1.79e-03 3.12e-03 4/30
Coenzyme transport and metabolism cog subcategory 2.71e-02 4.15e-02 3/30
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 238

There are 30 genes in Module 238

Gene Member Table (30)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0117 RSP_0117 CDS None chromosome 1 1830270 1832843 - Cytochrome c oxidase, subunit I (NCBI) False
RSP_0864 RSP_0864 CDS None chromosome 1 2615616 2616209 + Puative heme-binding hypothetical protein (NCBI) False
RSP_0918 RSP_0918 CDS None chromosome 1 2668563 2668760 - hypothetical protein (NCBI) False
RSP_0951 RSP_0951 CDS None chromosome 1 2704729 2704950 - hypothetical protein (NCBI) False
RSP_1319 RSP_1319 CDS None chromosome 1 3091328 3092008 + possible invasion protein (NCBI) False
RSP_1816 RSP_1816 CDS None chromosome 1 404461 405999 - Mg chelatase-related protein (NCBI) False
RSP_1822 RSP_1822 CDS None chromosome 1 412976 414520 + hypothetical protein (NCBI) False
RSP_1872 RSP_1872 CDS None chromosome 1 469645 471459 - Glycosyl transferase, family 2 (NCBI) False
RSP_1968 RSP_1968 CDS None chromosome 1 559600 560490 + Possible integrase/recombinase (NCBI) False
RSP_1992 RSP_1992 CDS None chromosome 1 588944 590125 + hypothetical protein (NCBI) False
RSP_2033 RSP_2033 CDS None chromosome 1 630298 630576 + hypothetical protein (NCBI) False
RSP_2059 RSP_2059 CDS None chromosome 1 651823 656844 - Potential phage tail tape measure protein (NCBI) False
RSP_2153 RSP_2153 CDS None chromosome 1 755838 756644 - hypothetical protein (NCBI) False
RSP_2186 RSP_2186 CDS None chromosome 1 792833 794218 - Transcriptional Regulator, MerR family (NCBI) False
RSP_2378 cypC CDS None chromosome 1 1005921 1007243 - putative fatty acid beta hydroxylase (cytochrome P450) (NCBI) False
RSP_2413 lig2 CDS None chromosome 1 1043632 1045233 - putative ATP-dependent DNA Ligase (NCBI) False
RSP_2497 RSP_2497 CDS None chromosome 1 1141281 1141934 - ATPase (NCBI) False
RSP_2501 RSP_2501 CDS None chromosome 1 1144947 1145786 - hypothetical protein (NCBI) False
RSP_2769 RSP_2769 CDS None chromosome 1 1416968 1417939 - probable 5,10-methylenetetrahydrofolate reductase (NCBI) False
RSP_2770 RSP_2770 CDS None chromosome 1 1417926 1418219 - hypothetical protein (NCBI) False
RSP_2930 RSP_2930 CDS None chromosome 1 1607702 1608325 - hypothetical protein (NCBI) False
RSP_2988 RSP_2988 CDS None chromosome 1 1679197 1679961 - Pirin-related protein (NCBI) False
RSP_3043 RSP_3043 CDS None chromosome 2 77673 78239 + hypothetical protein (NCBI) False
RSP_3322 acoR CDS None chromosome 2 383049 384884 - acetoin transcriptional regulator, sigma54 specific, AcoR (NCBI) True
RSP_3427 RSP_3427 CDS None chromosome 2 495626 497350 + hypothetical protein (NCBI) False
RSP_3433 RSP_3433 CDS None chromosome 2 505061 505534 + transcriptionalregulator, CopG family (NCBI) True
RSP_3608 RSP_3608 CDS None chromosome 2 704775 706394 - hypothetical protein (NCBI) False
RSP_3613 RSP_3613 CDS None chromosome 2 714525 722834 + Glycosyltransferase (NCBI) False
RSP_3614 RSP_3614 CDS None chromosome 2 722951 723301 - hypothetical protein (NCBI) False
RSP_3657 RSP_3657 CDS None chromosome 2 766355 767011 - putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase (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 238

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.