Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 44 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 44

There are 7 regulatory influences for Module 44

Regulator Table (7)
Regulator Name Type
RSP_1518 tf
RSP_3505 tf
RSP_3676 tf
RSP_3694 tf
RSP_0386 tf
RSP_1231 tf
RSP_1790 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
7808 5.10e-12 aagAAactCtggaaaAatgAgaaT
Loader icon
7809 1.20e-04 aCcCAcATaAaCaataTcaTTGAC
Loader icon
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 44 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Carbohydrate Metabolism kegg subcategory 7.14e-04 4.91e-03 6/27
Citrate cycle (TCA cycle) kegg pathway 1.00e-06 1.50e-05 4/27
Butanoate metabolism kegg pathway 8.00e-06 1.51e-04 4/27
Energy Metabolism kegg subcategory 1.72e-03 8.73e-03 5/27
Oxidative phosphorylation kegg pathway 8.90e-05 1.10e-03 4/27
Carbon fixation pathways in prokaryotes kegg pathway 4.00e-06 7.80e-05 4/27
Xenobiotics Biodegradation and Metabolism kegg subcategory 4.00e-06 7.90e-05 5/27
Toluene degradation kegg pathway 0.00e+00 0.00e+00 4/27
Environmental Information Processing kegg category 2.40e-05 3.75e-04 9/27
Membrane Transport kegg subcategory 3.07e-03 1.22e-02 5/27
ABC transporters kegg pathway 1.63e-03 8.42e-03 5/27
Signal Transduction kegg subcategory 4.57e-04 3.62e-03 4/27
Two-component system kegg pathway 4.57e-04 3.62e-03 4/27
Microbial metabolism in diverse environments kegg pathway 3.07e-03 1.22e-02 5/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 5.15e-04 9.96e-04 17/27
Energy production and conversion cog subcategory 1.84e-02 2.88e-02 4/27
Carbohydrate transport and metabolism cog subcategory 6.90e-05 1.75e-04 7/27
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 44

There are 27 genes in Module 44

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_1142 RSP_1142 CDS None chromosome 1 2903442 2903849 - hypothetical membrane protein (NCBI) False
RSP_1373 RSP_1373 CDS None chromosome 1 3151955 3153127 + Major facilitator superfamily (MFS) transporter (NCBI) False
RSP_1689 RSP_1689 CDS None chromosome 1 279224 280048 + hypothetical protein (NCBI) False
RSP_2250 RSP_2250 CDS None chromosome 1 866363 867091 - hypothetical protein (NCBI) False
RSP_2539 RSP_2539 CDS None chromosome 1 1182882 1184018 + ABC transporter, ATPase subunit (NCBI) False
RSP_2992 RSP_2992 CDS None chromosome 1 1684595 1685206 - hypothetical protein (NCBI) False
RSP_3143 RSP_3143 CDS None chromosome 2 193691 194032 - hypothetical protein (NCBI) False
RSP_3144 RSP_3144 CDS None chromosome 2 194042 195040 - hypothetical protein (NCBI) False
RSP_3145 ttdB CDS None chromosome 2 195037 195717 - Putative Tartrate dehydratase beta subunit (NCBI) False
RSP_3146 ttdA CDS None chromosome 2 195681 196643 - Putative Tartrate dehydratase alpha subunit (NCBI) False
RSP_3147 sdhA CDS None chromosome 2 196640 198403 - putative succinate dehydrogenase/fumarate reductase, flavoprotein subunit (NCBI) False
RSP_3148 RSP_3148 CDS None chromosome 2 198405 198749 - putative succinate dehydrogenase cytochrome b-556 subunit (NCBI) False
RSP_3149 RSP_3149 CDS None chromosome 2 198746 199081 - putative succinate dehydrogenase membrane anchor (NCBI) False
RSP_3150 frdB CDS None chromosome 2 199085 199813 - Succinate dehydrogenase/fumarate reductase Fe-S protein subunit (NCBI) False
RSP_3334 RSP_3334 CDS None chromosome 2 398053 398670 - HyuE hydantoin racemase (NCBI) False
RSP_3335 RSP_3335 CDS None chromosome 2 398710 399546 - ABC spermidine/putrescine transporter, inner membrane subunit (NCBI) False
RSP_3336 RSP_3336 CDS None chromosome 2 399548 400411 - ABC spermidine/putrescine transporter, inner membrane subunit (NCBI) False
RSP_3500 RSP_3500 CDS None chromosome 2 579125 580141 - ABC sugar transporter, periplasmic binding protein (NCBI) False
RSP_3501 RSP_3501 CDS None chromosome 2 580176 581159 - ABC sugar transporter, inner membrane subunit (NCBI) False
RSP_3502 RSP_3502 CDS None chromosome 2 581156 582166 - ABC sugar transporter, inner membrane subunit (NCBI) False
RSP_3503 RSP_3503 CDS None chromosome 2 582159 583634 - ABC sugar transporter, fused ATPase domains (NCBI) False
RSP_3505 RSP_3505 CDS None chromosome 2 583851 584789 + transcriptional regulator, DeoR family (NCBI) True
RSP_3506 RSP_3506 CDS None chromosome 2 584793 586322 + probable sugar kinase, EGGY family protein (NCBI) False
RSP_3574 hutH CDS None chromosome 2 668567 670138 - putative histidine ammonia-lyase (NCBI) False
RSP_3675 RSP_3675 CDS None chromosome 2 794257 795174 - Esterase/lipase/thioesterase (NCBI) False
RSP_3676 RSP_3676 CDS None chromosome 2 795171 795896 - transcriptional regulator, GntR family (NCBI) True
RSP_3677 RSP_3677 CDS None chromosome 2 796023 797102 + ABC sugar transporter, ATPase 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.