Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 95 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 95

There are 2 regulatory influences for Module 95

Regulator Table (2)
Regulator Name Type
RSP_2730 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
7910 1.40e-15 tgcgCAca.Aa.GgAtccTGtcaA
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7911 2.40e-05 AAAaTtaacGaCcAAtCAATC
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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 95 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Amino Acid Metabolism kegg subcategory 1.20e-04 1.38e-03 7/27
Histidine metabolism kegg pathway 0.00e+00 8.00e-06 4/27
Environmental Information Processing kegg category 1.79e-02 3.89e-02 5/27
Membrane Transport kegg subcategory 3.07e-03 1.22e-02 5/27
ABC transporters kegg pathway 1.63e-03 8.42e-03 5/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 2.68e-03 4.01e-03 4/27
Amino acids and amines tigr sub1role 0.00e+00 0.00e+00 4/27

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Information storage and processing cog category 1.28e-02 2.04e-02 7/27
Metabolism cog category 1.71e-02 2.69e-02 14/27
Transcription cog subcategory 2.23e-03 3.84e-03 5/27
Amino acid transport and metabolism cog subcategory 4.60e-04 9.08e-04 8/27
Secondary metabolites biosynthesis, transport and catabolism cog subcategory 3.68e-03 6.20e-03 3/27
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 95

There are 27 genes in Module 95

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0182 RSP_0182 DUMMY None chromosome 1 0 0 + None False
RSP_0610 RSP_0610 CDS None chromosome 1 2349479 2350285 - Putative 3-oxoacyl-(acyl-carrier-protein) reductase (NCBI) False
RSP_0796 cobQ CDS None chromosome 1 2539186 2540631 + cobyric acid synthase (NCBI) False
RSP_1434 RSP_1434 CDS None chromosome 1 12843 13823 - Putative Zn-dependent oxidoreductase (NCBI) False
RSP_1758 RSP_1758 CDS None chromosome 1 340889 342208 - Probable succinyl-diaminopimelate desuccinylase (NCBI) False
RSP_2632 argI CDS None chromosome 1 1271615 1272541 - Arginase (NCBI) False
RSP_2730 RSP_2730 CDS None chromosome 1 1380472 1380798 + Transcriptional regulator, ArsR family (NCBI) True
RSP_2853 RSP_2853 CDS None chromosome 1 1450705 1451346 - Transcriptional regulator, TetR family (NCBI) True
RSP_2854 RSP_2854 CDS None chromosome 1 1449545 1450705 - Cation/multidrug efflux pump, Membrane fusion protein (MFP) family (NCBI) False
RSP_2855 RSP_2855 CDS None chromosome 1 1446268 1449534 - Cation/multidrug efflux pump, RND superfamily (NCBI) False
RSP_2932 hutC CDS None chromosome 1 1609892 1610578 - Histidine utilization repressor, gntR family (NCBI) True
RSP_2933 hutF CDS None chromosome 1 1610578 1611957 - Formiminoglutamate deiminase (NCBI) False
RSP_2934 hutI CDS None chromosome 1 1612029 1613216 + Imidazolone-5-propionate hydrolase (NCBI) False
RSP_2935 hutH CDS None chromosome 1 1613216 1614739 + Probable histidine ammonia-lyase (NCBI) False
RSP_2936 hutU CDS None chromosome 1 1614750 1617476 + Urocanase (NCBI) False
RSP_3298 RSP_3298 CDS None chromosome 2 357349 358290 + transcriptional regulator, LysR family (NCBI) True
RSP_3403 RSP_3403 CDS None chromosome 2 469194 470036 - hypothetical protein (NCBI) False
RSP_3404 RSP_3404 CDS None chromosome 2 470287 471384 + hypothetical protein (NCBI) False
RSP_3405 gntR CDS None chromosome 2 471417 472136 + transcriptional regulator, GntR family (NCBI) True
RSP_3520 RSP_3520 CDS None chromosome 2 599523 601145 - ABC peptide transporter, fused ATPase domains (NCBI) False
RSP_3522 RSP_3522 CDS None chromosome 2 601149 602027 - ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_3523 RSP_3523 CDS None chromosome 2 602038 603003 - ABC peptide transporter, inner membrane subunit (NCBI) False
RSP_3524 RSP_3524 CDS None chromosome 2 603069 604673 - ABC peptide transporter, periplasmic binding protein (NCBI) False
RSP_3525 RSP_3525 CDS None chromosome 2 604763 606370 - ABC peptide transporter, periplasmic binding protein (NCBI) False
RSP_3526 RSP_3526 CDS None chromosome 2 606532 608004 + Amidase (NCBI) False
RSP_3527 RSP_3527 CDS None chromosome 2 608012 609046 + Probable acetylpolyamine aminohydrolase (NCBI) False
RSP_3584 RSP_3584 CDS None chromosome 2 678040 678414 + 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 95

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.