Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 77 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 77

There are 7 regulatory influences for Module 77

Regulator Table (7)
Regulator Name Type
RSP_1607 tf
RSP_2867 tf
RSP_2494 tf
RSP_1077 tf
RSP_3064 tf
RSP_1231 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
7874 8.50e-05 tcTgatc..gcAaaaAa.A.c
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7875 1.30e+03 CAtaATgCA.g.aatcg.ATgAA
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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 77 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Carbohydrate transport and metabolism cog subcategory 2.95e-02 4.49e-02 4/32
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 77

There are 32 genes in Module 77

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0118 RSP_0118 CDS None chromosome 1 1832840 1833814 - Cytochrome c oxidase, subunit IIc (NCBI) False
RSP_0607 RSP_0607 CDS None chromosome 1 2347737 2348597 + sigma 24 (NCBI) True
RSP_1602 RSP_1602 CDS None chromosome 1 199574 200845 - TRAP-T family transporter, DctM (12TMs) subunit (NCBI) False
RSP_1604 RSP_1604 CDS None chromosome 1 200870 201355 - TRAP-T family transporter, DctQ (4TMs) subunit (NCBI) False
RSP_1605 RSP_1605 CDS None chromosome 1 201425 202399 - TRAP-T family transporter, periplasmic binding protein, DctP (NCBI) False
RSP_1607 RSP_1607 CDS None chromosome 1 203237 204139 - Putative regulatory protein, GntR family (NCBI) True
RSP_1636 RSP_1636 CDS None chromosome 1 229655 234661 - phage-related protein, probable phage tail tape meausure protein, lambda family (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_2182 betI CDS None chromosome 1 788078 788662 + transcriptional regulator, BetI (NCBI) True
RSP_2183 betB CDS None chromosome 1 788659 790110 + Betaine aldehyde dehydrogenase (NCBI) False
RSP_2184 betA CDS None chromosome 1 790120 791766 + Choline dehydrogenase (NCBI) False
RSP_2555 RSP_2555 CDS None chromosome 1 1198838 1199098 + hypothetical protein (NCBI) False
RSP_2556 RSP_2556 CDS None chromosome 1 1199109 1199582 + hypothetical protein (NCBI) False
RSP_2750 RSP_2750 CDS None chromosome 1 1401018 1401476 + hypothetical protein (NCBI) False
RSP_2753 RSP_2753 CDS None chromosome 1 1402642 1403139 + hypothetical protein (NCBI) False
RSP_2755 RSP_2755 CDS None chromosome 1 1404223 1404648 + hypothetical protein (NCBI) False
RSP_2792 RSP_2792 CDS None chromosome 1 1529470 1531152 - putative monooxygenase alpha subunit (NCBI) False
RSP_2796 RSP_2796 CDS None chromosome 1 1525750 1526772 - hypothetical protein (NCBI) False
RSP_2798 groEL3 CDS None chromosome 1 1523230 1524861 - Putative chaperonin groEL (NCBI) False
RSP_2944 RSP_2944 CDS None chromosome 1 1624843 1625454 - hypothetical protein (NCBI) False
RSP_2995 RSP_2995 CDS None chromosome 1 1691779 1692888 - possible phage major capsid protein, gp36 (NCBI) False
RSP_3012 RSP_3012 CDS None chromosome 2 44920 45330 - Probable transposase (NCBI) False
RSP_3065 RSP_3065 CDS None chromosome 2 105579 106712 + Putative transporter, Major facilitator superfamily (MFS) (NCBI) False
RSP_3114 RSP_3114 CDS None chromosome 2 159306 160385 - hypothetical protein (NCBI) False
RSP_3259 RSP_3259 CDS None chromosome 2 316328 316927 - Transcription antitermination protein (NCBI) False
RSP_3380 RSP_3380 CDS None chromosome 2 444078 444743 + hypothetical protein (NCBI) False
RSP_3393 RSP_3393 CDS None chromosome 2 458274 459068 - ABC opine/polyamine transporter, inner membrane subunit (NCBI) False
RSP_3420 RSP_3420 CDS None chromosome 2 488557 490131 + Methyl-accepting chemotaxis protein (NCBI) False
RSP_3421 RSP_3421 CDS None chromosome 2 490128 490703 + hypothetical protein (NCBI) False
RSP_3605 RSP_3605 CDS None chromosome 2 700112 701212 + FAD-dependent pyridine nucleotide-disulphide oxidoreductase (NCBI) False
RSP_3788 RSP_3788 CDS None chromosome 2 900754 901200 - 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 77

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.