Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 161 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 161

There are 9 regulatory influences for Module 161

Regulator Table (9)
Regulator Name Type
RSP_0443 tf
RSP_1092 tf
RSP_2533 tf
RSP_2410 tf
RSP_3179 tf
RSP_2351 tf
RSP_0601 tf
RSP_1032 tf
RSP_2130 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
8042 1.60e-07 AgattT.TtgagTcATatcAtAt
Loader icon
8043 3.90e+00 cTgaTA.Gg.ataA
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 161 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 1.76e-02 3.83e-02 4/28
ABC transporters kegg pathway 1.06e-02 2.71e-02 4/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Biosynthesis of cofactors, prosthetic groups, and carriers tigr mainrole 5.66e-03 7.69e-03 3/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 3.06e-04 6.33e-04 12/28
Inorganic ion transport and metabolism cog subcategory 1.63e-03 2.86e-03 5/28
General function prediction only cog subcategory 1.34e-02 2.14e-02 6/28
Function unknown cog subcategory 4.32e-03 7.23e-03 6/28
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 161

There are 28 genes in Module 161

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0124 RSP_0124 CDS None chromosome 1 1838097 1838369 + hypothetical protein (NCBI) False
RSP_0244 RSP_0244 CDS None chromosome 1 1967154 1967999 - Predicted glutamine amidotransferases (NCBI) False
RSP_0442 RSP_0442 CDS None chromosome 1 2173313 2174359 - putative aminotransferase (NCBI) False
RSP_0443 RSP_0443 CDS None chromosome 1 2174442 2174909 - Rrf2 family transcriptional regulator (NCBI) True
RSP_0525 RSP_0525 CDS None chromosome 1 2263490 2264149 + hypothetical protein (NCBI) False
RSP_0601 rpoH2 CDS None chromosome 1 2342488 2343366 - sigma factor RpoH2 (Sigma-32 group (NCBI) True
RSP_0850 RSP_0850 CDS None chromosome 1 2600381 2601358 + conserved hypothetical transmembrane protein (NCBI) False
RSP_1409 RSP_1409 CDS None chromosome 1 3185942 3186412 - Beta-Ig-H3/Fasciclin (NCBI) False
RSP_1545 RSP_1545 CDS None chromosome 1 136202 137710 - Probable thiol oxidoreductase with 2 cytochrome c heme-binding sites (NCBI) False
RSP_1546 bfr CDS None chromosome 1 137889 138374 - Bacterioferritin (NCBI) False
RSP_1547 RSP_1547 CDS None chromosome 1 138364 138618 - probable bacterioferritin-associated ferredoxin (NCBI) False
RSP_1825 tldD CDS None chromosome 1 416542 417963 - probable modulator of DNA gyrase (NCBI) False
RSP_1852 RSP_1852 CDS None chromosome 1 446347 447426 + hypothetical protein (NCBI) False
RSP_1948 RSP_1948 CDS None chromosome 1 546042 546398 - Protein of unknown function, HesB/YadR/YfhF (NCBI) False
RSP_1949 RSP_1949 CDS None chromosome 1 546482 546844 - hypothetical protein (NCBI) False
RSP_2359 RSP_2359 CDS None chromosome 1 985754 986074 - hypothetical protein (NCBI) False
RSP_2360 RSP_2360 CDS None chromosome 1 986071 987264 - putative head portal protein, HK97 family (NCBI) False
RSP_2361 RSP_2361 CDS None chromosome 1 987339 989156 - putative integrase/resolvase recombinase protein phage-related integrase (NCBI) False
RSP_2388 RSP_2388 CDS None chromosome 1 1017366 1017866 - hypothetical protein (NCBI) False
RSP_2783 lipA CDS None chromosome 1 1431034 1431996 + lipoic acid synthetase (NCBI) False
RSP_3078 RSP_3078 CDS None chromosome 2 121170 121454 - hypothetical protein (NCBI) False
RSP_3117 RSP_3117 CDS None chromosome 2 162726 163409 + hypothetical protein (NCBI) False
RSP_3141 RSP_3141 CDS None chromosome 2 191591 191899 + hypothetical protein (NCBI) False
RSP_3142 RSP_3142 CDS None chromosome 2 191896 193626 + Na+/solute symporter (NCBI) False
RSP_3567 znuB CDS None chromosome 2 663999 664781 - ABC zinc tranporter, inner membrane subunit ZnuB (NCBI) False
RSP_3568 znuC CDS None chromosome 2 664774 665505 - ABC zinc transporter, ATPase subunit ZnuC (NCBI) False
RSP_3569 zur CDS None chromosome 2 665502 666005 - Zinc-uptake regulator, Zur (NCBI) False
RSP_3571 znuA CDS None chromosome 2 666062 667099 + ABC zinc transporter, periplasmic binding protein ZnuA (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.