Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 175 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 175

There are 18 regulatory influences for Module 175

Regulator Table (18)
Regulator Name Type
RSP_1590 tf
RSP_1866 tf
RSP_1952 tf
RSP_2730 tf
RSP_2838 tf
RSP_2171 tf
RSP_3665 tf
RSP_2867 tf
RSP_2533 tf
RSP_3606 tf
RSP_3324 tf
RSP_1577 tf
RSP_2610 tf
RSP_1092 tf
RSP_2889 tf
RSP_0722 tf
RSP_1032 tf
RSP_2939 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
8070 4.90e-06 AAAAaATccCccGaaTTcTCCCCG
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8071 3.10e-01 at.cAgcC.CGtCcCgGGTGcGta
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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 175 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism of Other Amino Acids kegg subcategory 1.88e-03 9.18e-03 3/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Posttranslational modification, protein turnover, chaperones cog subcategory 1.48e-02 2.34e-02 3/32
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 175

There are 32 genes in Module 175

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0182 RSP_0182 DUMMY None chromosome 1 0 0 + None False
RSP_0302 ureG CDS None chromosome 1 2032887 2033510 - Urease accessory protein G (NCBI) False
RSP_0303 ureF CDS None chromosome 1 2033507 2034139 - Urease accessory protein UreF (NCBI) False
RSP_0304 ureE CDS None chromosome 1 2034136 2034684 - urease accessory protein UreE (NCBI) False
RSP_0305 RSP_0305 CDS None chromosome 1 2034681 2035100 - hypothetical protein (NCBI) False
RSP_0306 RSP_0306 CDS None chromosome 1 2036968 2037840 + Class I diheme cytochrome c (NCBI) False
RSP_0329 RSP_0329 CDS None chromosome 1 2056160 2057170 + GAF sensor diguanylate cyclase (GGDEF) (NCBI) False
RSP_0406 RSP_0406 CDS None chromosome 1 2139213 2140256 - periplasmic sensor diguanylate cyclase (GGDEF) (NCBI) False
RSP_0407 RSP_0407 CDS None chromosome 1 2140469 2141464 - putative lactate dehydrogenase (NCBI) False
RSP_0803 DppF CDS None chromosome 1 2547213 2547968 - ABC dipeptide transporter, ATPase subunit DppF (NCBI) False
RSP_0894 RSP_0894 CDS None chromosome 1 2645693 2646151 + hypothetical protein (NCBI) False
RSP_0895 RSP_0895 CDS None chromosome 1 2646151 2646921 + phosphodiesterase-like (NCBI) False
RSP_0943 yhxA CDS None chromosome 1 2693657 2695039 + probable adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI) False
RSP_1086 sdh CDS None chromosome 1 2843735 2844790 + saccharopine dehydrogenase (NAD+, L-lysine forming) (NCBI) False
RSP_1377 RSP_1377 CDS None chromosome 1 3156070 3156738 - Carbonic anhydrase (NCBI) False
RSP_1378 RSP_1378 CDS None chromosome 1 3156854 3157237 + hypothetical protein (NCBI) False
RSP_1379 RSP_1379 CDS None chromosome 1 3157254 3158693 + Cytosol aminopeptidase (NCBI) False
RSP_1380 RSP_1380 CDS None chromosome 1 3158690 3159505 + hypothetical protein (NCBI) False
RSP_1590 RSP_1590 CDS None chromosome 1 182539 183996 - two component, sigma54 specific, transcriptional regulator, fis family (NCBI) True
RSP_1946 RSP_1946 CDS None chromosome 1 543683 544864 - Cytochrome P450 hydroxylase (NCBI) False
RSP_2012 RSP_2012 CDS None chromosome 1 612944 613420 - NUDIX hydrolase, MutT (NCBI) False
RSP_2168 RSP_2168 CDS None chromosome 1 772144 772500 + hypothetical protein (NCBI) False
RSP_2188 RSP_2188 CDS None chromosome 1 795537 795890 - hypothetical protein (NCBI) False
RSP_2252 RSP_2252 CDS None chromosome 1 868100 869077 - Threonine dehydratase (NCBI) False
RSP_2253 RSP_2253 CDS None chromosome 1 869074 869898 - predicted hydrolases or acyltransferases (NCBI) False
RSP_2883 pgm CDS None chromosome 1 1554749 1556383 - Probable phosphoglucomutase/phosphomannomutase (NCBI) False
RSP_2898 RSP_2898 CDS None chromosome 1 1573457 1573915 - putative DNA polymerase III chi subunit (NCBI) False
RSP_2899 RSP_2899 CDS None chromosome 1 1574019 1575488 - Probable cytosol aminopeptidase (NCBI) False
RSP_3246 RSP_3246 CDS None chromosome 2 303343 304893 + putative D-alanyl-D-alanine carboxypeptidase (NCBI) False
RSP_3381 RSP_3381 CDS None chromosome 2 444827 445801 - NAD(P)H -dependent quinone oxidoreductase (NCBI) False
RSP_3419 RSP_3419 CDS None chromosome 2 487758 488336 + hypothetical protein (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.

Comments for Module 175

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.