Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 176 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 176

There are 9 regulatory influences for Module 176

Regulator Table (9)
Regulator Name Type
RSP_2026 tf
RSP_2850 tf
RSP_2494 tf
RSP_1163 tf
RSP_3202 tf
RSP_1704 tf
RSP_3226 tf
RSP_0794 tf
RSP_0623 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
8072 1.20e+01 ttcAtGaaATgggAAGcGGGttG
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8073 2.40e+01 CtTCcccAtat.CCtGtcaa
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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 176 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Lipid Metabolism kegg subcategory 3.23e-03 1.27e-02 3/33

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 1.49e-02 2.36e-02 8/33
Transcription cog subcategory 2.18e-04 4.69e-04 7/33
Lipid transport and metabolism cog subcategory 2.39e-02 3.69e-02 3/33
Inorganic ion transport and metabolism cog subcategory 1.82e-02 2.85e-02 4/33
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 176

There are 33 genes in Module 176

Gene Member Table (33)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0113 RSP_0113 CDS None chromosome 1 1826723 1828219 + Phospholipase D/Transphosphatidylase (NCBI) False
RSP_0114 RSP_0114 CDS None chromosome 1 1828216 1828560 + hypothetical protein (NCBI) False
RSP_0429 RSP_0429 CDS None chromosome 1 2163545 2165401 + Probable ABC drug/toxin efflux transporter; fused ATPase and inner membrane subunits (NCBI) False
RSP_0511 RSP_0511 CDS None chromosome 1 2245560 2246135 + two component transcriptional regulator, LuxR family (NCBI) True
RSP_0765 RSP_0765 CDS None chromosome 1 2507492 2508133 - SAM-dependent methyltransferase (NCBI) False
RSP_0941 RSP_0941 CDS None chromosome 1 2691891 2692784 + ABC transporter, ATPase subunit (NCBI) False
RSP_0942 RSP_0942 CDS None chromosome 1 2692784 2693548 + ABC transporter, inner membrane subunit (NCBI) False
RSP_1524 RSP_1524 CDS None chromosome 1 110754 111419 + Nucleotidyltransferase family protein (NCBI) False
RSP_1566 RSP_1566 CDS None chromosome 1 156951 157640 + hypothetical protein (NCBI) False
RSP_1600 RSP_1600 CDS None chromosome 1 197835 198767 + possible transporter, DME family, DMT superfamily (NCBI) False
RSP_1922 RSP_1922 CDS None chromosome 1 519356 520768 + Transcriptional regulator, GntR family, with aminotransferase domain (NCBI) True
RSP_2003 yibQ CDS None chromosome 1 601039 602472 + YibQ protein (NCBI) False
RSP_2026 RSP_2026 CDS None chromosome 1 624857 625834 + transcriptional regulator, AraC family (NCBI) True
RSP_2160 gno CDS None chromosome 1 764032 764796 - Short-chain dehydrogenase/reductase (NCBI) False
RSP_3052 RSP_3052 CDS None chromosome 2 90873 91751 - transcriptional regulator, LysR family (NCBI) True
RSP_3053 RSP_3053 CDS None chromosome 2 91912 92841 + Possible dioxygenase/glyoxalase family protein (NCBI) False
RSP_3055 RSP_3055 CDS None chromosome 2 94475 94945 + transcriptional regulator, MarR family (NCBI) True
RSP_3085 RSP_3085 CDS None chromosome 2 130099 131748 + Conserved hypothetical membrane protein (NCBI) False
RSP_3086 RSP_3086 CDS None chromosome 2 132121 133437 - periplasmic sensor signal transduction histidine kinase (NCBI) False
RSP_3087 dgkA CDS None chromosome 2 131759 132139 + diacylglycerol kinase (NCBI) False
RSP_3088 RSP_3088 CDS None chromosome 2 133434 134093 - two component transcriptional regulator, winged helix family (NCBI) False
RSP_3157 RSP_3157 CDS None chromosome 2 207597 208721 - ABC transporter, inner membrane subunit (NCBI) False
RSP_3202 RSP_3202 CDS None chromosome 2 255489 256400 + transcriptional regulator, AraC family (NCBI) True
RSP_3215 RSP_3215 CDS None chromosome 2 269476 272856 - hypothetical protein (NCBI) False
RSP_3245 RSP_3245 CDS None chromosome 2 301985 303220 + Possible transporter, Major facilitator superfamily (MFS) (NCBI) False
RSP_3284 iolD CDS None chromosome 2 340942 342786 + Acetolactate synthase (NCBI) False
RSP_3377 RSP_3377 CDS None chromosome 2 441633 442517 + Glutathione S-transferase family protein (NCBI) False
RSP_3466 RSP_3466 CDS None chromosome 2 535219 536508 + hypothetical protein (NCBI) False
RSP_3467 RSP_3467 CDS None chromosome 2 536510 537532 + hypothetical protein (NCBI) False
RSP_3468 RSP_3468 CDS None chromosome 2 537525 538616 + hypothetical protein (NCBI) False
RSP_3469 RSP_3469 CDS None chromosome 2 538613 539614 + hypothetical protein (NCBI) False
RSP_3470 RSP_3470 CDS None chromosome 2 539611 540390 + hypothetical protein (NCBI) False
RSP_3629 RSP_3629 CDS None chromosome 2 741697 742512 + hypothetical protein (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 176

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.