Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 304 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 304

There are 12 regulatory influences for Module 304

Regulator Table (12)
Regulator Name Type
RSP_3684 tf
RSP_1607 tf
RSP_3676 tf
RSP_1660 tf
RSP_3418 tf
RSP_2932 tf
RSP_3001 tf
RSP_0511 tf
RSP_3055 tf
RSP_2922 tf
RSP_3616 tf
RSP_3464 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
8322 4.80e+04 AAACCTTA
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8323 6.20e+04 ACATGAAGA
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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 304 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
General function prediction only cog subcategory 1.73e-02 2.71e-02 7/36
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 304

There are 36 genes in Module 304

Gene Member Table (36)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0297 RSP_0297 CDS None chromosome 1 2026281 2026979 - ABC branched chain amino acid transporter, ATPase subunit (NCBI) False
RSP_0512 RSP_0512 CDS None chromosome 1 2246349 2249186 + multisensor hybrid histidine kinase (NCBI) False
RSP_0609 RSP_0609 CDS None chromosome 1 2348723 2349103 + hypothetical protein (NCBI) False
RSP_0856 btaA CDS None chromosome 1 2605905 2607155 + S-adenosylmethionine-diacylglycerol 3-amino-3-carboxypropyl transferase (NCBI) False
RSP_0938 RSP_0938 CDS None chromosome 1 2689471 2689698 + hypothetical protein (NCBI) False
RSP_1323 RSP_1323 CDS None chromosome 1 3096291 3096578 - hypothetical protein (NCBI) False
RSP_1500 RSP_1500 CDS None chromosome 1 87234 87776 - possible anti-sigma regulatory kinase (NCBI) False
RSP_1618 RSP_1618 CDS None chromosome 1 216210 216713 - hypothetical protein (NCBI) False
RSP_1651 RSP_1651 CDS None chromosome 1 245668 246105 - hypothetical protein (NCBI) False
RSP_1694 RSP_1694 CDS None chromosome 1 282869 283684 - Probable short-chain dehydrogenase/reductase (NCBI) False
RSP_1753 RSP_1753 CDS None chromosome 1 335207 337378 + hypothetical protein (NCBI) False
RSP_1954 RSP_1954 CDS None chromosome 1 550280 550546 + hypothetical protein (NCBI) False
RSP_2023 RSP_2023 CDS None chromosome 1 623291 623875 - hypothetical protein (NCBI) False
RSP_2068 RSP_2068 CDS None chromosome 1 661551 662390 - putative ClpP-like protease (NCBI) False
RSP_2070 RSP_2070 CDS None chromosome 1 663637 665346 - Putative Phage-related terminase (NCBI) False
RSP_2071 RSP_2071 CDS None chromosome 1 665348 665824 - hypothetical protein (NCBI) False
RSP_2259 RSP_2259 CDS None chromosome 1 876808 877245 - Transmembrane protein (NCBI) False
RSP_2441 tlpS CDS None chromosome 1 1074101 1075888 - Putative transducer like protein (NCBI) False
RSP_2769 RSP_2769 CDS None chromosome 1 1416968 1417939 - probable 5,10-methylenetetrahydrofolate reductase (NCBI) False
RSP_2813 mttB CDS None chromosome 1 1501478 1503019 - putative trimethylamine methyltransferase protein (NCBI) False
RSP_3014 RSP_3014 CDS None chromosome 2 46296 47048 - putative aldolase protein (NCBI) False
RSP_3018 RSP_3018 CDS None chromosome 2 49518 50690 - putative acyl-CoA dehydrogenase (NCBI) False
RSP_3096 RSP_3096 CDS None chromosome 2 139114 139422 - hypothetical protein (NCBI) False
RSP_3098 qoxB CDS None chromosome 2 141893 142678 - QoxB, Quinol oxidase subunit II (NCBI) False
RSP_3103 RSP_3103 CDS None chromosome 2 147245 147883 + hypothetical protein (NCBI) False
RSP_3104 fdh CDS None chromosome 2 147887 149071 + Putative Glutathione-dependent formaldehyde dehydrogenase (NCBI) False
RSP_3204 RSP_3204 CDS None chromosome 2 257830 258351 + putative Oxidoreductase (NCBI) False
RSP_3283 RSP_3283 CDS None chromosome 2 339755 340780 + myo-inositol 2-dehydrogenase (NCBI) False
RSP_3357 gpU CDS None chromosome 2 421946 422326 + putative phage tail protein U (NCBI) False
RSP_3358 gpX CDS None chromosome 2 422323 422535 + Phage tail component protein X (NCBI) False
RSP_3577 gvpG CDS None chromosome 2 673174 673407 - putative gas vesicle synthesis protein (NCBI) False
RSP_3659 RSP_3659 CDS None chromosome 2 767805 768647 - Predicted amidohydrolase (NCBI) False
RSP_3682 RSP_3682 CDS None chromosome 2 803449 803706 - hypothetical protein (NCBI) False
RSP_3774 RSP_3774 CDS None chromosome 2 914116 914637 - hypothetical protein (NCBI) False
RSP_3775 RSP_3775 CDS None chromosome 2 913652 914119 - hypothetical protein (NCBI) False
RSP_3814 RSP_3814 CDS None chromosome 2 12213 13130 + 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 304

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.