Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 130 Profile

GeneModule member RegulatorRegulator MotifMotif
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 130

There are 23 regulatory influences for Module 130

Regulator Table (23)
Regulator Name Type
RSP_1225 tf
RSP_0386 tf
RSP_0623 tf
RSP_1890 tf
RSP_3665 tf
RSP_2838 tf
RSP_1741 tf
RSP_1220 tf
RSP_2950 tf
RSP_2965 tf
RSP_2840 tf
RSP_1712 tf
RSP_0760 tf
RSP_2182 tf
RSP_0014 tf
RSP_3436 tf
RSP_2681 tf
RSP_0907 tf
RSP_1164 tf
RSP_1922 tf
RSP_2801 tf
RSP_0722 tf
RSP_0395 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
7980 1.60e-01 T.ttgGCtTGAaga.caggg
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7981 9.70e+03 Aa.AA.gAaaa
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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 130 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 2.36e-03 1.05e-02 12/28
Metabolism of Cofactors and Vitamins kegg subcategory 2.06e-02 4.32e-02 3/28
Membrane Transport kegg subcategory 1.76e-02 3.83e-02 4/28
ABC transporters kegg pathway 1.06e-02 2.71e-02 4/28
Global kegg category 1.93e-02 4.12e-02 9/28
Metabolism kegg subcategory 1.93e-02 4.12e-02 9/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Coenzyme transport and metabolism cog subcategory 2.15e-02 3.33e-02 3/28
General function prediction only cog subcategory 7.65e-04 1.42e-03 8/28
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 130

There are 28 genes in Module 130

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0445 RSP_0445 CDS None chromosome 1 2175719 2176303 + hypothetical protein (NCBI) False
RSP_0651 RSP_0651 CDS None chromosome 1 2389367 2390161 - Putative inositol monophosphatase protein (NCBI) False
RSP_0652 RSP_0652 CDS None chromosome 1 2390172 2391158 - UDP-glucose 4-epimerase (NCBI) False
RSP_0656 RSP_0656 CDS None chromosome 1 2394469 2396247 - Probable sodium/sulphate symporter (NCBI) False
RSP_0677 RSP_0677 CDS None chromosome 1 2418198 2419136 + Putative malonate transporter, mdcF, AEC family (NCBI) False
RSP_0702 RSP_0702 CDS None chromosome 1 2446450 2447556 - ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_0703 RSP_0703 CDS None chromosome 1 2447558 2448646 - ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_0781 RSP_0781 CDS None chromosome 1 2524376 2526562 + polyphosphate kinase (NCBI) False
RSP_0930 folC CDS None chromosome 1 2679301 2680575 + Folylpolyglutamate synthetase (NCBI) False
RSP_1049 pheAa CDS None chromosome 1 2808173 2808472 - putative chorismate mutase protein (NCBI) False
RSP_1065 RSP_1065 CDS None chromosome 1 2823196 2823939 + hypothetical protein (NCBI) False
RSP_1066 RSP_1066 CDS None chromosome 1 2823936 2824589 + Probable GTP-binding protein (NCBI) False
RSP_1156 RSP_1156 CDS None chromosome 1 2918891 2919652 + ABC transporter, ATPase subunit (NCBI) False
RSP_1289 RSP_1289 CDS None chromosome 1 3055890 3056822 - ABC branched chain amino acid family transporter, inner membrane subunit (NCBI) False
RSP_1569 RSP_1569 CDS None chromosome 1 161714 163087 - probable aminotransferase (NCBI) False
RSP_1623 RSP_1623 CDS None chromosome 1 219377 220213 + hypothetical protein (NCBI) False
RSP_1670 spoT/relA CDS None chromosome 1 260559 262676 + RelA/SpoT family protein (NCBI) False
RSP_2190 RSP_2190 CDS None chromosome 1 798472 798870 + hypothetical protein (NCBI) False
RSP_2458 RSP_2458 CDS None chromosome 1 1099436 1100182 - ABC transporter, ATPase subunit (NCBI) False
RSP_2542 RSP_2542 CDS None chromosome 1 1185748 1186587 + ATPase (NCBI) False
RSP_2707 uppS CDS None chromosome 1 1355798 1356541 + Undecaprenyl pyrophosphate synthase (NCBI) False
RSP_2708 cdsA CDS None chromosome 1 1356538 1357359 + Phosphatidate cytidylyltransferase (NCBI) False
RSP_2904 pdxA1 CDS None chromosome 1 1581398 1582366 + Putative4-hydroxythreonine-4-phosphate dehydrogenase 1 (NCBI) False
RSP_3136 RSP_3136 CDS None chromosome 2 183381 185744 - hypothetical protein (NCBI) False
RSP_3644 RSP_3644 CDS None chromosome 2 751763 753184 - Metal dependent phosphohydrolase (NCBI) False
RSP_3645 RSP_3645 CDS None chromosome 2 753448 754851 - hypothetical protein (NCBI) False
RSP_3758 RSP_3758 CDS None chromosome 2 885800 887131 - Cytosine-specific DNA methylase (NCBI) False
RSP_3759 RSP_3759 CDS None chromosome 2 884950 885807 - Putative endonuclease (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.

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.