Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 356 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 356

There are 14 regulatory influences for Module 356

Regulator Table (14)
Regulator Name Type
RSP_3341 tf
RSP_1866 tf
RSP_3165 tf
RSP_1660 tf
RSP_2533 tf
RSP_3238 tf
RSP_1055 tf
RSP_0794 tf
RSP_0755 tf
RSP_2351 tf
RSP_3621 tf
RSP_2950 tf
RSP_0999 tf
RSP_3748 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
8410 1.70e-02 atgacacttCaGtGAaaaGA
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8411 3.80e+01 ATATCtggcAAAGGtCAT
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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 356 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 1.91e-03 9.24e-03 6/31

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.10e-02 1.77e-02 10/31
Function unknown cog subcategory 7.86e-03 1.29e-02 6/31
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 356

There are 31 genes in Module 356

Gene Member Table (31)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0821 RSP_0821 CDS None chromosome 1 2566932 2567702 - Esterase/lipase/thioesterase (NCBI) False
RSP_0939 RSP_0939 CDS None chromosome 1 2689898 2690677 + hypothetical protein (NCBI) False
RSP_1045 trmD CDS None chromosome 1 2805259 2806095 - tRNA (guanine-N1-)-methyltransferase (NCBI) False
RSP_1101 RSP_1101 CDS None chromosome 1 2859434 2861137 - hypothetical protein (NCBI) False
RSP_1149 gltD CDS None chromosome 1 2912514 2913941 - Glutamate synthase (beta subunit) (NCBI) False
RSP_1152 rnd CDS None chromosome 1 2916201 2916815 + Ribonuclease D (NCBI) False
RSP_1154 RSP_1154 CDS None chromosome 1 2917765 2918379 + hypothetical protein (NCBI) False
RSP_1155 RSP_1155 CDS None chromosome 1 2918403 2918894 + OstA-like protein (NCBI) False
RSP_1830 surf-1 CDS None chromosome 1 421826 422497 + Surf1 protein (NCBI) False
RSP_1847 PurD CDS None chromosome 1 438151 439413 + Phosphoribosylamine--glycine ligase (NCBI) False
RSP_1865 RSP_1865 CDS None chromosome 1 463305 464327 - ketol-acid reductoisomerase (NCBI) False
RSP_1866 RSP_1866 CDS None chromosome 1 464457 464912 + Transcriptional regulator, AsnC family (NCBI) True
RSP_1867 RSP_1867 CDS None chromosome 1 464909 465367 + transcriptional regulator, AsnC family (NCBI) True
RSP_2191 pccA CDS None chromosome 1 799508 801595 + Propionyl-CoA carboxylase alpha subunit (NCBI) False
RSP_2284 RSP_2284 CDS None chromosome 1 905665 906750 + Histidinol-phosphate aminotransferase (NCBI) False
RSP_2327 RSP_2327 CDS None chromosome 1 951213 951752 - hypothetical protein (NCBI) False
RSP_2328 mreC CDS None chromosome 1 951745 952647 - Rod shape-determining protein, MreC (NCBI) False
RSP_2619 trmU CDS None chromosome 1 1257890 1259029 - tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) False
RSP_2748 RSP_2748 CDS None chromosome 1 1398481 1398876 - possible transcriptional regulator, CopG family (NCBI) False
RSP_2790 RSP_2790 CDS None chromosome 1 1532219 1532440 + hypothetical protein (NCBI) False
RSP_2912 RSP_2912 CDS None chromosome 1 1589910 1590716 + Predicted pyrophosphatase (NCBI) False
RSP_2970 RSP_2970 CDS None chromosome 1 1654702 1655958 - Transporter, Major facilitator superfamily (MFS) (NCBI) False
RSP_3170 RSP_3170 CDS None chromosome 2 224025 224636 + Demethylmenaquinone methyltransferase (NCBI) False
RSP_3171 RSP_3171 CDS None chromosome 2 224637 225503 + 3-hydroxyisobutyrate dehydrogenase (NCBI) False
RSP_3172 RSP_3172 CDS None chromosome 2 225503 226336 + hypothetical protein (NCBI) False
RSP_3200 RSP_3200 CDS None chromosome 2 252907 254151 + Molecular chaperone, DnaK (NCBI) False
RSP_3227 RSP_3227 CDS None chromosome 2 285991 287013 + Lysine 2,3-aminomutase (NCBI) False
RSP_3344 RSP_3344 CDS None chromosome 2 408103 409575 - PAS sensor diguanylate cyclase (NCBI) False
RSP_3593 RSP_3593 CDS None chromosome 2 685745 686470 - hypothetical protein (NCBI) False
RSP_3607 RSP_3607 CDS None chromosome 2 702698 704725 + hypothetical protein (NCBI) False
RSP_3777 RSP_3777 CDS None chromosome 2 911914 912498 - 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 356

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.