Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 223 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 223

There are 11 regulatory influences for Module 223

Regulator Table (11)
Regulator Name Type
DVU1561
DVU1964
combiner
DVU3167 tf
DVU2275 tf
DVU1949 tf
DVU0309
DVU0653
combiner
DVU2036
DVU2275
combiner
DVU1788
DVU2275
combiner
DVU2557
DVU2195
combiner
DVU0653 tf
DVU2909
DVU0653
combiner
DVU2909
DVU2275
combiner

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.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (2)
Motif Id e-value Consensus Motif Logo RegPredict
425 1.20e-02 GggcgcAaGgC
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RegPredict
426 8.40e+03 gGCaTcGtATcgAcGaatCaC
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RegPredict
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 223 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Aminoacyl-tRNA biosynthesis kegg pathway 6.90e-05 1.01e-03 3/28
Metabolic pathways kegg pathway 1.50e-03 6.28e-03 9/28
Biosynthesis of secondary metabolites kegg pathway 2.31e-03 7.81e-03 5/28
Amino Acid Metabolism kegg subcategory 2.85e-04 3.16e-03 6/28
Metabolism of Cofactors and Vitamins kegg subcategory 1.69e-03 1.05e-02 4/28
Translation kegg subcategory 4.11e-03 1.98e-02 3/28
Metabolism kegg subcategory 6.00e-06 1.46e-04 16/28
Metabolism kegg category 5.00e-06 1.01e-04 17/28
Global kegg category 6.00e-06 1.17e-04 16/28
Metabolism kegg category 3.32e-04 3.59e-03 11/28
Amino Acid Metabolism kegg subcategory 1.98e-02 4.21e-02 3/28
Metabolism of Cofactors and Vitamins kegg subcategory 1.63e-03 9.46e-03 4/28
Translation kegg subcategory 4.11e-03 1.54e-02 3/28
Aminoacyl-tRNA biosynthesis kegg pathway 6.90e-05 1.26e-03 3/28
Global kegg category 1.81e-03 9.91e-03 9/28
Metabolism kegg subcategory 1.81e-03 9.91e-03 9/28
Metabolic pathways kegg pathway 1.50e-03 9.02e-03 9/28
Biosynthesis of secondary metabolites kegg pathway 2.31e-03 1.14e-02 5/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Protein synthesis tigr mainrole 1.50e-03 1.15e-02 4/28
Protein synthesis tigr mainrole 1.50e-03 2.67e-03 4/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Metabolism cog category 1.64e-02 2.72e-02 11/28
Poorly characterized cog category 1.18e-02 2.02e-02 7/28
Translation, ribosomal structure and biogenesis cog subcategory 2.94e-02 4.63e-02 3/28
Energy production and conversion cog subcategory 2.33e-02 3.74e-02 4/28
Amino acid transport and metabolism cog subcategory 2.79e-02 4.41e-02 4/28
Function unknown cog subcategory 2.34e-02 3.77e-02 3/28
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 223

There are 28 genes in Module 223

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0135 CDS 2794158 chromosome 171562 172473 - hypothetical protein DVU0135 False
DVU0136 CDS 2794159 chromosome 172638 172856 - hypothetical protein DVU0136 False
DVU0141 CDS 2796557 chromosome 176335 177009 + M50 family peptidase False
DVU0323 folD CDS 2794446 chromosome 366622 367482 + bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase False
DVU0414 CDS 2795177 chromosome 463867 465186 + NADP-dependent malic enzyme-like protein False
DVU0660 CDS 2794246 chromosome 731288 731854 + phosphodiesterase False
DVU0724 CDS 2794129 chromosome 806523 807929 - sodium/alanine symporter family protein False
DVU0726 tgt CDS 2794131 chromosome 810938 812065 - queuine tRNA-ribosyltransferase False
DVU0795 purC CDS 2794517 chromosome 880193 881089 - phosphoribosylaminoimidazole-succinocarboxamide synthase False
DVU0796 hisD CDS 2794518 chromosome 881106 882416 - histidinol dehydrogenase False
DVU1029 hisC CDS 2794526 chromosome 1133410 1134531 - histidinol-phosphate aminotransferase False
DVU1060 CDS 2794772 chromosome 1160947 1162050 - glycosyl transferase group 1 family protein False
DVU1091 CDS 2794070 chromosome 1195859 1196965 + hypothetical protein DVU1091 False
DVU1220 CDS 2796678 chromosome 1311642 1312466 + nitroreductase family protein False
DVU1540 purU CDS 2793690 chromosome 1606991 1607845 - formyltetrahydrofolate deformylase False
DVU1693 gltX-1 CDS 2795827 chromosome 1769611 1770585 - glutamyl-tRNA synthetase False
DVU1827 CDS 2793488 chromosome 1892330 1893553 + diaminopimelate aminotransferase False
DVU1942 CDS 2793514 chromosome 2015131 2017044 + DAK2 and DegV domain-containing protein False
DVU1978 CDS 2795992 chromosome 2053213 2054535 - Na+/H+ antiporter family protein False
DVU2055 metG CDS 2796479 chromosome 2131143 2133134 - methionyl-tRNA synthetase False
DVU2210 CDS 2795357 chromosome 2305040 2306767 + hypothetical protein False
DVU2436 CDS 2795427 chromosome 2540394 2541026 + hypothetical protein DVU2436 False
DVU2471 CDS 2795653 chromosome 2578425 2579723 + oxidoreductase, selenocysteine-containing False
DVU2493 CDS 2795461 chromosome 2604855 2606243 + iron-sulfur cluster-binding protein False
DVU2552 gltX CDS 2796126 chromosome 2663659 2665050 - glutamyl-tRNA synthetase False
DVU2892 CDS 2793922 chromosome 2989179 2989979 + GTP cyclohydrolase False
DVU3208 CDS 2796206 chromosome 3374162 3375145 + membrane protein False
DVU3389 topA CDS 2796408 chromosome 3563643 3565925 + DNA topoisomerase I 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 223

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.