Organism : Rhodobacter sphaeroides 2.4.1 | Module List:
Module 262 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 262

There are 11 regulatory influences for Module 262

Regulator Table (11)
Regulator Name Type
RSP_0394 tf
RSP_2610 tf
RSP_0698 tf
RSP_1663 tf
RSP_2853 tf
RSP_2922 tf
RSP_0032 tf
RSP_1231 tf
RSP_1139 tf
RSP_1890 tf
RSP_0316 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
8242 3.40e+03 AAAACcctggCttT
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8243 3.70e+04 AACAGAAA
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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 262 is enriched for following functions.

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.37e-02 2.18e-02 8/28
Cell wall/membrane/envelope biogenesis cog subcategory 3.69e-03 6.21e-03 4/28
Posttranslational modification, protein turnover, chaperones cog subcategory 9.22e-03 1.50e-02 3/28
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 262

There are 28 genes in Module 262

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
RSP_0017 RSP_0017 CDS None chromosome 1 1718215 1719102 - ABC spermidine/putrescine transporter, inner membrane subunit (NCBI) False
RSP_0167 RSP_0167 CDS None chromosome 1 1882687 1883118 + hypothetical protein (NCBI) False
RSP_0237 argE CDS None chromosome 1 1957724 1958887 - acetylornithine deacetylase (NCBI) False
RSP_0243 RSP_0243 CDS None chromosome 1 1965738 1966766 + putative lipoprotein (NCBI) False
RSP_0252 RSP_0252 CDS None chromosome 1 1976110 1976763 - Protein-L-isoaspartatecarboxylmethyltransferase (NCBI) False
RSP_0668 RSP_0668 CDS None chromosome 1 2409516 2410064 - OmpA/MotB family protein (NCBI) False
RSP_0698 fnrL CDS None chromosome 1 2441421 2442167 - Crp-Fnr regulatory protein (FnrL) (NCBI) True
RSP_0839 RSP_0839 CDS None chromosome 1 2587887 2588375 - Predicted secreted periplasmic protein (NCBI) False
RSP_0932 ctpA CDS None chromosome 1 2681206 2682552 - Peptidase family S41 (NCBI) False
RSP_1097 RSP_1097 CDS None chromosome 1 2855241 2856587 - putative zinc protease (NCBI) False
RSP_1098 RSP_1098 CDS None chromosome 1 2856667 2857194 - hypothetical protein (NCBI) False
RSP_1126 rnr CDS None chromosome 1 2889366 2891624 - Exoribonuclease R (NCBI) False
RSP_1199 RSP_1199 CDS None chromosome 1 2969569 2970171 - secreted conserved hypothetical protein (NCBI) False
RSP_1345 RSP_1345 CDS None chromosome 1 3114534 3114956 + hypothetical protein (NCBI) False
RSP_1399 RSP_1399 CDS None chromosome 1 3176985 3177845 + hypothetical protein (NCBI) False
RSP_1464 RSP_1464 CDS None chromosome 1 50364 51050 - putative periplasmic thiol-disulphide interchange protein (DsbA family) (NCBI) False
RSP_1465 RSP_1465 CDS None chromosome 1 51047 51577 - hypothetical protein (NCBI) False
RSP_2136 RSP_2136 CDS None chromosome 1 736430 737644 + hypothetical protein (NCBI) False
RSP_2167 RSP_2167 CDS None chromosome 1 771407 772147 + hypothetical protein (NCBI) False
RSP_2309 RSP_2309 CDS None chromosome 1 931046 932101 - hypothetical protein (NCBI) False
RSP_2549 exoQ CDS None chromosome 1 1192424 1193713 - putative polysaccharide polymerase (NCBI) False
RSP_2550 exoK CDS None chromosome 1 1193730 1194512 - endo-beta-1,3-1,4-glycanase protein (NCBI) False
RSP_2633 ccmF CDS None chromosome 1 1273029 1274999 + Cytochrome c maturation protein, CcmF (NCBI) False
RSP_2682 fabD CDS None chromosome 1 1327641 1328573 + Malonyl-CoA-acyl carrier protein transacylase (NCBI) False
RSP_2771 RSP_2771 CDS None chromosome 1 1418489 1419625 + putative Exopolyphosphatase (NCBI) False
RSP_2962 RSP_2962 CDS None chromosome 1 1644753 1646252 + Methylmalonic acid semialdehyde dehydrogenase (NCBI) False
RSP_2967 RSP_2967 CDS None chromosome 1 1651098 1652234 - Probable transporter, Major facilitator superfamily (MFS) (NCBI) False
RSP_3229 RSP_3229 CDS None chromosome 2 287499 288887 - Membrane-bound lytic murein transglycosylase B (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 262

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.