Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 342 Profile

GeneModule member RegulatorRegulator MotifMotif
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 342

There are 9 regulatory influences for Module 342

Regulator Table (9)
Regulator Name Type
RSP_3445 tf
RSP_3464 tf
RSP_3322 tf
RSP_0386 tf
RSP_3238 tf
RSP_1607 tf
RSP_1518 tf
RSP_2867 tf
RSP_3064 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
8386 2.60e-02 tctcCtTaggTCgcAtTtTtT
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8387 1.90e+00 TctggcgGaAagg.cttac.gAac
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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 342 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Membrane Transport kegg subcategory 2.03e-02 4.26e-02 4/29
ABC transporters kegg pathway 1.24e-02 3.00e-02 4/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Transport and binding proteins tigr mainrole 3.78e-03 5.38e-03 3/29

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 342

There are 29 genes in Module 342

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0181 RSP_0181 CDS None chromosome 1 1897527 1898462 - ABC nitrate/sulfonate/bicarbonate transporter, inner membrane subunit (NCBI) False
RSP_0221 RSP_0221 CDS None chromosome 1 1936160 1938697 + plasma membrane H+-transporting two-sector ATPase, C subunit (NCBI) False
RSP_0620 RSP_0620 CDS None chromosome 1 2356138 2356488 + hypothetical protein (NCBI) False
RSP_0838 RSP_0838 CDS None chromosome 1 2586898 2587890 - putative DNA polymerase III, delta subunit / DNA binding (NCBI) False
RSP_1320 flhA CDS None chromosome 1 3092012 3094078 + Flagellar biosynthesis pathway, component FlhA (NCBI) False
RSP_1333 RSP_1333 CDS None chromosome 1 3102195 3102518 - hypothetical protein (NCBI) False
RSP_1334 RSP_1334 CDS None chromosome 1 3102508 3102786 - possible chemotactic signal-response protein CheL (NCBI) False
RSP_1335 RSP_1335 CDS None chromosome 1 3102890 3105109 + hypothetical protein (NCBI) False
RSP_1336 RSP_1336 CDS None chromosome 1 3105119 3105787 + Possible FlgD protein (NCBI) False
RSP_1616 RSP_1616 CDS None chromosome 1 215064 215519 - hypothetical protein (NCBI) False
RSP_1620 RSP_1620 CDS None chromosome 1 217383 217676 + hypothetical protein (NCBI) False
RSP_1656 RSP_1656 CDS None chromosome 1 250745 250930 + hypothetical protein (NCBI) False
RSP_1658 RSP_1658 CDS None chromosome 1 251121 251453 + hypothetical protein (NCBI) False
RSP_1659 RSP_1659 CDS None chromosome 1 251453 251848 + hypothetical protein (NCBI) False
RSP_2260 ydjG CDS None chromosome 1 877250 878347 - hypothetical protein (NCBI) False
RSP_3057 RSP_3057 CDS None chromosome 2 97408 98499 - ABC proline/glycine betaine transporter, ATPase subunit (NCBI) False
RSP_3058 RSP_3058 CDS None chromosome 2 98492 99403 - ABC proline/glycine betaine transporter, inner membrane subunit (NCBI) False
RSP_3059 RSP_3059 CDS None chromosome 2 99471 100472 - ABC proline/glycine betaine transporter, periplasmic substrate-binding protein (NCBI) False
RSP_3110 RSP_3110 CDS None chromosome 2 155515 156171 + Putative Glutathione S-transferase (NCBI) False
RSP_3360 RSP_3360 CDS None chromosome 2 423689 424477 + Adenine specific DNA methyltransferase, D12 class (NCBI) False
RSP_3406 pdxA CDS None chromosome 2 472183 473169 - 4-hydroxythreonine-4-phosphate dehydrogenase 2 (NCBI) False
RSP_3445 RSP_3445 CDS None chromosome 2 515634 516269 - transcriptional regulator, GntR family (NCBI) True
RSP_3518 RSP_3518 CDS None chromosome 2 597387 598172 + ABC polyamine/opine transporter, inner membrane subunit (NCBI) False
RSP_3544 RSP_3544 CDS None chromosome 2 634618 634920 + hypothetical protein (NCBI) False
RSP_3545 RSP_3545 CDS None chromosome 2 634975 635529 + hypothetical protein (NCBI) False
RSP_3661 RSP_3661 CDS None chromosome 2 768699 769694 - TRAP-T family transporter, periplasmic binding protein (NCBI) False
RSP_3662 RSP_3662 CDS None chromosome 2 769762 771042 - TRAP-T family transporter, large (12TMs) inner membrane subunit (NCBI) False
RSP_3663 RSP_3663 CDS None chromosome 2 771039 771593 - TRAP-T family transporter, small (4TMs) inner membrane subunit (NCBI) False
RSP_3781 RSP_3781 CDS None chromosome 2 907304 909466 - putative phage terminase large subunit (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.

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.