Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 325 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 325

There are 3 regulatory influences for Module 325

Regulator Table (3)
Regulator Name Type
RSP_3676 tf
RSP_1231 tf
RSP_2922 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
8358 1.30e-02 tgAtcgTtacaaAtTgaga
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8359 2.00e+03 acaTTac.aCAcac.CgtaAa
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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 325 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
ABC transporters kegg pathway 1.86e-02 3.98e-02 4/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 1.45e-03 2.56e-03 12/32
General function prediction only cog subcategory 8.38e-03 1.37e-02 7/32
Function unknown cog subcategory 3.26e-02 4.93e-02 5/32
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 325

There are 32 genes in Module 325

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0213 RSP_0213 CDS None chromosome 1 1925447 1927102 - Phage terminase-like protein large subunit (NCBI) False
RSP_0214 RSP_0214 CDS None chromosome 1 1927099 1927404 - possible uncharacterized phage protein (NCBI) False
RSP_0613 RSP_0613 CDS None chromosome 1 2351902 2352414 + hypothetical protein (NCBI) False
RSP_0614 RSP_0614 CDS None chromosome 1 2352461 2352757 + hypothetical protein (NCBI) False
RSP_0617 RSP_0617 CDS None chromosome 1 2354634 2355188 + hypothetical protein (NCBI) False
RSP_0960 RSP_0960 CDS None chromosome 1 2717534 2718826 - alcohol dehydrogenase (NCBI) False
RSP_1084 RSP_1084 CDS None chromosome 1 2840745 2841962 + putative glycosyl transferase, group 1 family protein (NCBI) False
RSP_1142 RSP_1142 CDS None chromosome 1 2903442 2903849 - hypothetical membrane protein (NCBI) False
RSP_1318 RSP_1318 CDS None chromosome 1 3089074 3091032 + hypothetical protein (NCBI) False
RSP_1444 RSP_1444 CDS None chromosome 1 26527 27375 + ABC sugar transporter, inner membrane subunit (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_1820 RSP_1820 CDS None chromosome 1 409736 410245 - hypothetical protein (NCBI) False
RSP_1932 RSP_1932 CDS None chromosome 1 530439 531635 + hypothetical protein (NCBI) False
RSP_1953 RSP_1953 CDS None chromosome 1 549413 550153 - Transcriptional regulator, CRP/FNR family (NCBI) False
RSP_1960 RSP_1960 DUMMY None chromosome 1 0 0 + None False
RSP_2105 RSP_2105 CDS None chromosome 1 706074 706580 - hypothetical protein (NCBI) False
RSP_2217 RSP_2217 CDS None chromosome 1 829071 829550 - hypothetical protein (NCBI) False
RSP_2244 RSP_2244 CDS None chromosome 1 860903 861283 + hypothetical protein (NCBI) False
RSP_2280 RSP_2280 CDS None chromosome 1 900561 902483 + PAS sensor hybrid histidine kinase (NCBI) False
RSP_2363 RSP_2363 CDS None chromosome 1 990482 991246 + Short-chain dehydrogenase/reductase (NCBI) False
RSP_2371 RSP_2371 CDS None chromosome 1 997596 998342 + 3-oxoacyl-(acyl-carrier protein) reductase / Short-chain dehydrogenase/reductase SDR (NCBI) False
RSP_2703 RSP_2703 CDS None chromosome 1 1351475 1352980 - ABC dipeptide transporter, periplasmic binding protein (NCBI) False
RSP_2720 RSP_2720 CDS None chromosome 1 1370494 1371102 + Putative LysE/RhtB family amino acid efflux pump (NCBI) False
RSP_3000 RSP_3000 CDS None chromosome 1 1697025 1697336 - hypothetical protein (NCBI) False
RSP_3051 RSP_3051 CDS None chromosome 2 88598 90577 + Putative phosphatase (NCBI) False
RSP_3252 RSP_3252 CDS None chromosome 2 310159 311937 - ABC peptide transporter, fused ATPase domains (NCBI) False
RSP_3257 RSP_3257 CDS None chromosome 2 314543 315463 - ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_3260 amiC CDS None chromosome 2 316924 317985 - Putative negative amidase regulator, AmiC (NCBI) False
RSP_3545 RSP_3545 CDS None chromosome 2 634975 635529 + hypothetical protein (NCBI) False
RSP_3575 gvpK CDS None chromosome 2 670202 670534 - putative gas vesicle synthesis 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 325

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.