Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 285 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 285

There are 15 regulatory influences for Module 285

Regulator Table (15)
Regulator Name Type
RSP_3322 tf
RSP_1014 tf
RSP_3124 tf
RSP_3029 tf
RSP_1990 tf
RSP_0186 tf
RSP_0386 tf
RSP_1704 tf
RSP_1890 tf
RSP_2351 tf
RSP_0018 tf
RSP_2026 tf
RSP_1055 tf
RSP_3109 tf
RSP_3042 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
8284 9.40e-06 tgGtATcaacAtaA.AgGc
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8285 4.10e+00 gcgcATCcaGtcGgacaagCatAc
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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 285 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Poorly characterized cog category 2.81e-02 4.29e-02 10/35
Transcription cog subcategory 8.63e-03 1.41e-02 5/35
Lipid transport and metabolism cog subcategory 2.91e-02 4.43e-02 3/35
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 285

There are 35 genes in Module 285

Gene Member Table (35)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0018 RSP_0018 CDS None chromosome 1 1719530 1720933 - Putative transcriptional regulator, gntR family (NCBI) True
RSP_0019 RSP_0019 CDS None chromosome 1 1721018 1721245 + hypothetical protein (NCBI) False
RSP_0204 RSP_0204 CDS None chromosome 1 1919694 1920605 + metallo-beta-lactamase family protein (NCBI) False
RSP_0354 RSP_0354 CDS None chromosome 1 2084288 2084740 + hypothetical protein (NCBI) False
RSP_0424 RSP_0424 CDS None chromosome 1 2155955 2156563 + hypothetical protein (NCBI) False
RSP_0595 RSP_0595 CDS None chromosome 1 2336088 2336603 - hypothetical protein (NCBI) False
RSP_0606 RSP_0606 CDS None chromosome 1 2347274 2347747 + Putative redox protein (NCBI) False
RSP_0709 cpdB CDS None chromosome 1 2453997 2455889 + 2',3'-cyclic-nucleotide 2'-phosphodiesterase (NCBI) False
RSP_0985 RSP_0985 CDS None chromosome 1 2742390 2744087 - adenine deaminase (NCBI) False
RSP_1000 RSP_1000 CDS None chromosome 1 2758394 2759191 + hypothetical protein (NCBI) False
RSP_1067 fixR CDS None chromosome 1 2824593 2825369 - Short-chain alcohol dehydrogenase (NCBI) False
RSP_1083 RSP_1083 CDS None chromosome 1 2841944 2842645 - two component transcriptional regulator, winged helix family (NCBI) False
RSP_1297 RSP_1297 CDS None chromosome 1 3065797 3066711 + transcriptional regulator, LysR family (NCBI) True
RSP_1405 RSP_1405 CDS None chromosome 1 3181832 3182719 + ROK family protein (NCBI) False
RSP_1433 RSP_1433 CDS None chromosome 1 12125 12823 - hypothetical protein (NCBI) False
RSP_1778 RSP_1778 CDS None chromosome 1 362979 364256 + TPR domain protein (NCBI) False
RSP_1779 ispE CDS None chromosome 1 364249 365085 + Putative 4-diphosphocytidyl-2C-methyl-D-erythritol kinase (NCBI) False
RSP_1780 RSP_1780 CDS None chromosome 1 365227 365712 + hypothetical protein (NCBI) False
RSP_1966 RSP_1966 CDS None chromosome 1 558661 559536 - possible ISSod13, transposase (NCBI) False
RSP_2003 yibQ CDS None chromosome 1 601039 602472 + YibQ protein (NCBI) False
RSP_2122 mtbC CDS None chromosome 1 723139 723837 - Putative dimethylamine corrinoid protein (NCBI) False
RSP_2396 RSP_2396 CDS None chromosome 1 1023737 1024738 - hypothetical protein (NCBI) False
RSP_2433 cheY2 CDS None chromosome 1 1066514 1066900 - Chemotaxis response regulator, CheY2 (NCBI) False
RSP_2649 RSP_2649 CDS None chromosome 1 1292063 1292749 - Putative Zn-dependent protease (NCBI) False
RSP_2674 RSP_2674 CDS None chromosome 1 1317485 1317832 - hypothetical protein (NCBI) False
RSP_2731 ArsH CDS None chromosome 1 1381081 1381794 + arsenical resistance protein, ArsH (NCBI) False
RSP_2765 RSP_2765 CDS None chromosome 1 1411144 1411416 + hypothetical protein (NCBI) False
RSP_3109 RSP_3109 CDS None chromosome 2 154964 155428 - transcriptional regulator, MarR family (NCBI) True
RSP_3111 RSP_3111 CDS None chromosome 2 156203 156901 + Putative Glutathione S-transferase (NCBI) False
RSP_3112 RSP_3112 CDS None chromosome 2 156912 157388 + hypothetical protein (NCBI) False
RSP_3218 RSP_3218 CDS None chromosome 2 274459 275151 + Putative oxidoreductase NAD protein (NCBI) False
RSP_3260 amiC CDS None chromosome 2 316924 317985 - Putative negative amidase regulator, AmiC (NCBI) False
RSP_3424 RSP_3424 CDS None chromosome 2 492281 493075 + hypothetical protein (NCBI) False
RSP_3787 RSP_3787 CDS None chromosome 2 901298 901768 - hypothetical protein (NCBI) False
RSP_3805 RSP_3805 CDS None chromosome 2 922803 923801 + possible integrase (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 285

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.