Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 195 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 195

There are 10 regulatory influences for Module 195

Regulator Table (10)
Regulator Name Type
RSP_1231 tf
RSP_1191 tf
RSP_0316 tf
RSP_0698 tf
RSP_0927 tf
RSP_1435 tf
RSP_1990 tf
RSP_3606 tf
RSP_2853 tf
RSP_0087 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
8110 2.40e+01 aAAGGgcG
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8111 1.10e+03 AaTgTGCcaAaatAT
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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 195 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Butanoate metabolism kegg pathway 3.55e-04 3.02e-03 3/32
Amino Acid Metabolism kegg subcategory 1.05e-02 2.69e-02 5/32
Global kegg category 1.95e-02 4.14e-02 10/32
Metabolism kegg subcategory 1.95e-02 4.14e-02 10/32
Biosynthesis of secondary metabolites kegg pathway 1.18e-03 6.93e-03 7/32
Microbial metabolism in diverse environments kegg pathway 7.44e-03 2.15e-02 5/32

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.18e-02 1.89e-02 9/32
Signal transduction mechanisms cog subcategory 9.51e-03 1.54e-02 4/32
Lipid transport and metabolism cog subcategory 2.16e-02 3.34e-02 3/32
General function prediction only cog subcategory 2.75e-02 4.20e-02 6/32
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 195

There are 32 genes in Module 195

Gene Member Table (32)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0451 alaS CDS None chromosome 1 2181723 2184374 - Alanyl-tRNA synthetase, class IIc (NCBI) False
RSP_0745 RSP_0745 CDS None chromosome 1 2489502 2490668 + acetyl-CoA acetyltransferase (NCBI) False
RSP_0747 RSP_0747 CDS None chromosome 1 2490768 2491490 + Short-chain dehydrogenase/reductase (NCBI) False
RSP_0872 def1 CDS None chromosome 1 2620676 2621209 + Formylmethionine deformylase (NCBI) False
RSP_0936 dapF CDS None chromosome 1 2686494 2687324 - Diaminopimelate epimerase (NCBI) False
RSP_0940 RSP_0940 CDS None chromosome 1 2690826 2691833 + ABC transporter, periplasmic substrate binding protein (NCBI) False
RSP_0955 RSP_0955 CDS None chromosome 1 2711808 2713379 - 5'-nucleotidase (NCBI) False
RSP_1056 RSP_1056 CDS None chromosome 1 2814112 2815512 - periplasmic sensor signal transduction histidine kinase (NCBI) False
RSP_1412 RSP_1412 CDS None chromosome 2 926940 929573 - TRAP-T family transporter with fused DctQ/DctM subunits (NCBI) False
RSP_1567 RSP_1567 CDS None chromosome 1 157676 160243 - Probable sensory transduction histidine kinase (NCBI) False
RSP_1628 RSP_1628 CDS None chromosome 1 224676 225674 + possible sensor histidine protein kinase (NCBI) False
RSP_1990 RSP_1990 CDS None chromosome 1 587069 587500 - Transcriptional regulator, AsnC family (NCBI) True
RSP_2008 argD CDS None chromosome 1 609595 610776 + Acetylornithine Aminotransferase class-III (NCBI) False
RSP_2288 RSP_2288 CDS None chromosome 1 910229 911404 + hypothetical protein (NCBI) False
RSP_2289 RSP_2289 CDS None chromosome 1 911408 912985 + Outer membrane protein, OmpA/MotB family (NCBI) False
RSP_2431 RSP_2431 CDS None chromosome 1 1064635 1065927 - putative O-acetylhomoserine sulfhydrylase (NCBI) False
RSP_2461 fabG CDS None chromosome 1 1102236 1102973 + 3-oxoacyl-(acyl-carrier protein) reductase (NCBI) False
RSP_2536 rhlE CDS None chromosome 1 1178520 1180076 - ATP-dependent helicase, DEAD-box (NCBI) False
RSP_2549 exoQ CDS None chromosome 1 1192424 1193713 - putative polysaccharide polymerase (NCBI) False
RSP_2633 ccmF CDS None chromosome 1 1273029 1274999 + Cytochrome c maturation protein, CcmF (NCBI) False
RSP_2729 RSP_2729 CDS None chromosome 1 1379593 1380177 + Probable Restriction endonuclease (NCBI) False
RSP_2845 RSP_2845 CDS None chromosome 1 1460728 1463199 + putative penicillin acylase (penicillin amidase) (NCBI) False
RSP_2923 RSP_2923 CDS None chromosome 1 1601836 1603020 + ABC branched amino acid transporter family, periplasmic substrate-binding protein (NCBI) False
RSP_2967 RSP_2967 CDS None chromosome 1 1651098 1652234 - Probable transporter, Major facilitator superfamily (MFS) (NCBI) False
RSP_3186 RSP_3186 CDS None chromosome 2 238728 239405 - hypothetical protein (NCBI) False
RSP_3231 RSP_3231 CDS None chromosome 2 289521 291119 + ABC peptide transporter, periplasmic binding protein (NCBI) False
RSP_3241 RSP_3241 CDS None chromosome 2 298522 299196 - Two-component transcriptional regulator, winged helix family (NCBI) False
RSP_3325 RSP_3325 CDS None chromosome 2 388457 389962 + Polysaccharide export transporter, PST Family (NCBI) False
RSP_3345 RSP_3345 CDS None chromosome 2 409838 411136 + hypothetical protein (NCBI) False
RSP_3604 RSP_3604 CDS None chromosome 2 699059 700111 + Rhodanese-like protein (NCBI) False
RSP_3831 cox15 CDS None chromosome 2 25912 27087 + putative cytochrome oxidase assembly factor (NCBI) False
RSP_4047 pdhAa CDS None chromosome 1 1124389 1125378 - Pyruvate dehydrogenase E1 component, alpha 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.

Comments for Module 195

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.