Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 208 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 208

There are 8 regulatory influences for Module 208

Regulator Table (8)
Regulator Name Type
RSP_1890 tf
RSP_0623 tf
RSP_1164 tf
RSP_1739 tf
RSP_1225 tf
RSP_0722 tf
RSP_0760 tf
RSP_1712 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
8136 2.70e-04 TTtatcctta.ctAaaaaAA
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8137 1.30e+00 CCC.tt.ctGtTG.tt.gaGg
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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 208 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolism kegg category 1.62e-02 3.59e-02 10/27
Carbohydrate Metabolism kegg subcategory 1.30e-05 2.26e-04 8/27
Citrate cycle (TCA cycle) kegg pathway 0.00e+00 0.00e+00 5/27
Pyruvate metabolism kegg pathway 1.80e-04 1.88e-03 3/27
Propanoate metabolism kegg pathway 1.00e-06 3.60e-05 4/27
Energy Metabolism kegg subcategory 1.72e-03 8.73e-03 5/27
Carbon fixation pathways in prokaryotes kegg pathway 9.80e-05 1.17e-03 3/27
Amino Acid Metabolism kegg subcategory 2.01e-02 4.24e-02 4/27
Global kegg category 4.67e-03 1.59e-02 10/27
Metabolism kegg subcategory 4.67e-03 1.59e-02 10/27
Metabolic pathways kegg pathway 9.52e-03 2.51e-02 9/27
Biosynthesis of secondary metabolites kegg pathway 5.10e-05 6.96e-04 8/27
Microbial metabolism in diverse environments kegg pathway 8.00e-06 1.54e-04 8/27

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Energy metabolism tigr mainrole 3.57e-04 6.53e-04 5/27
TCA cycle 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
Metabolism cog category 1.19e-04 2.83e-04 18/27
Energy production and conversion cog subcategory 6.95e-04 1.31e-03 6/27
Amino acid transport and metabolism cog subcategory 9.43e-03 1.53e-02 6/27
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 208

There are 27 genes in Module 208

Gene Member Table (27)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0009 RSP_0009 CDS None chromosome 1 1711869 1712738 + hypothetical protein (NCBI) False
RSP_0189 RSP_0189 CDS None chromosome 1 1905803 1907140 - NADPH-dependent glutamate synthase beta chain and related oxidoreductase (NCBI) False
RSP_0190 accB CDS None chromosome 1 1907274 1907906 + Biotin carboxyl carrier protein, AccB (NCBI) False
RSP_0191 accC CDS None chromosome 1 1907914 1909260 + Biotin carboxylase (NCBI) False
RSP_0192 aat CDS None chromosome 1 1909280 1909924 + possible leucyl/phenylalanyl-tRNA--protein transferase (NCBI) False
RSP_0962 RSP_0962 CDS None chromosome 1 2721358 2722746 - Dihydrolipoamide dehydrogenase (NCBI) False
RSP_0963 RSP_0963 CDS None chromosome 1 2722861 2723256 - Inner membrane protein (NCBI) False
RSP_0964 sucB CDS None chromosome 1 2723312 2724844 - Dihydrolipoamide transsuccinylase (NCBI) False
RSP_0965 sucA CDS None chromosome 1 2724844 2727822 - 2-oxoglutarate dehydrogenase E1 component (RefSeq) False
RSP_0966 sucD CDS None chromosome 1 2727862 2728746 - Succinyl-CoA synthetase, alpha subunit (NCBI) False
RSP_0967 sucC CDS None chromosome 1 2728751 2729944 - Succinyl-CoA synthetase, beta subunit (NCBI) False
RSP_0970 RSP_0970 CDS None chromosome 1 2732163 2733020 + Putative citrate lyase beta chain (NCBI) False
RSP_1060 rnpA CDS None chromosome 1 2818049 2818462 + Ribonuclease P protein component (NCBI) False
RSP_1061 RSP_1061 CDS None chromosome 1 2818459 2818713 + hypothetical protein (NCBI) False
RSP_1071 moaE CDS None chromosome 1 2827569 2828009 - Molybdopterin converting factor subunit 2 (NCBI) False
RSP_1074 uvrC CDS None chromosome 1 2829001 2830872 - Excinuclease ABC, C subunit (NCBI) False
RSP_1622 RSP_1622 CDS None chromosome 1 220172 221230 - Putative DNA-binding protein (NCBI) False
RSP_1624 RSP_1624 CDS None chromosome 1 221252 221896 - hypothetical protein (NCBI) False
RSP_1975 RSP_1975 CDS None chromosome 1 565102 566898 - aminopeptidase P (NCBI) False
RSP_2297 atpA CDS None chromosome 1 919693 921231 + F0F1-type ATP synthase alpha subunit (NCBI) False
RSP_2423 RSP_2423 CDS None chromosome 1 1055245 1055541 + putative Heat shock protein 15 (HSP15) (NCBI) False
RSP_2924 RSP_2924 CDS None chromosome 1 1603149 1603931 + ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) False
RSP_2925 RSP_2925 CDS None chromosome 1 1604024 1604734 + ABC branched-chain amino acid transporter family, ATPase subunit (NCBI) False
RSP_2926 RSP_2926 CDS None chromosome 1 1604738 1605748 + ABC branched-chain amino acid transporter family, inner membrane subunit (NCBI) False
RSP_2928 RSP_2928 CDS None chromosome 1 1607045 1607644 + 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

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.