Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 270 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 270

There are 8 regulatory influences for Module 270

Regulator Table (8)
Regulator Name Type
DVU1949 tf
DVU1063 tf
DVU2799 tf
DVU2788
DVU0916		 combiner
DVU2909
DVU1517		 combiner
DVU1754
DVU1561		 combiner
DVU1788
DVU0804		 combiner
DVU2832
DVU1745		 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
515 4.00e+03 gCAAcGcaACC
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 RegPredict
516 2.10e+01 AttCgtTgaC.aaaTtCTG.AAG
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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 270 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Two-component system kegg pathway 3.03e-04 2.61e-03 4/28
Metabolism of Cofactors and Vitamins kegg subcategory 1.13e-02 3.85e-02 3/28
Signal Transduction kegg subcategory 3.03e-04 3.22e-03 4/28
Metabolism kegg subcategory 7.57e-03 3.08e-02 11/28
Global kegg category 7.57e-03 4.30e-02 11/28
Environmental Information Processing kegg category 1.88e-02 4.06e-02 4/28
Signal Transduction kegg subcategory 3.03e-04 3.42e-03 4/28
Two-component system kegg pathway 3.03e-04 3.42e-03 4/28

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
ATP binding molecular_function 2.99e-02 3.83e-02 5/28

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cell envelope tigr mainrole 5.06e-04 6.09e-03 3/28
Cell envelope tigr mainrole 5.06e-04 1.01e-03 3/28

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Cellular processes and signaling cog category 1.97e-03 3.36e-02 12/28
Information storage and processing cog category 1.53e-02 2.55e-02 6/28
Cellular processes and signaling cog category 7.87e-03 1.38e-02 10/28
Translation, ribosomal structure and biogenesis cog subcategory 5.87e-03 1.05e-02 4/28
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 270

There are 28 genes in Module 270

Gene Member Table (28)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0422 CDS 2795215 chromosome 475147 478365 - sensory box protein False
DVU0527 maF CDS 2794893 chromosome 600433 601065 + Maf-like protein False
DVU0668 CDS 2794692 chromosome 739843 741429 + methyl-accepting chemotaxis protein False
DVU0786 CDS 2794811 chromosome 872482 874269 - penicillin-binding protein False
DVU1044 guaB CDS 2795265 chromosome 1146685 1148142 - inosine-5`-monophosphate dehydrogenase False
DVU1240 CDS 2794417 chromosome 1328303 1328710 - hypothetical protein DVU1240 False
DVU1251 CDS 2795032 chromosome 1337597 1337815 - hypothetical protein DVU1251 False
DVU1258 glnN CDS 2794604 chromosome 1343777 1345957 - glutamine synthetase, type III False
DVU1273 CDS 2794263 chromosome 1364359 1365933 - type II/III secretion system protein False
DVU1429 ychF CDS 2794690 chromosome 1503735 1504835 - GTP-dependent nucleic acid-binding protein EngD False
DVU1694 CDS 2795829 chromosome 1770879 1771088 - C4-type zinc finger DksA/TraR family protein False
DVU1703 CDS 2795785 chromosome 1777728 1781027 - type I restriction-modification enzyme, R subunit False
DVU1878 ltaE CDS 2793547 chromosome 1946235 1947257 - threonine aldolase False
DVU1879 CDS 2793548 chromosome 1947269 1948369 - glycosyl transferase group 1 family protein False
DVU1890 hemC CDS 2794701 chromosome 1962409 1963356 + porphobilinogen deaminase False
DVU1897 glyS CDS 2794708 chromosome 1970475 1972565 - glycyl-tRNA synthetase subunit beta False
DVU1898 glyQ CDS 2794709 chromosome 1972583 1973452 - glycyl-tRNA synthetase subunit alpha False
DVU1949 nifA-1 CDS 2793521 chromosome 2021083 2022672 - nif-specific regulatory protein True
DVU1951 CDS 2796186 chromosome 2023272 2025122 - indolepyruvate ferredoxin oxidoreductase subunit alpha False
DVU2043 CDS 2794539 chromosome 2120862 2122463 + hypothetical protein DVU2043 False
DVU2317 CDS 2795277 chromosome 2411334 2413103 + methyl-accepting chemotaxis protein False
DVU2567 CDS 2796260 chromosome 2680076 2680780 - hypothetical protein DVU2567 True
DVU2579 CDS 2794992 chromosome 2698344 2698973 + hypothetical protein False
DVU2678 CDS 2795049 chromosome 2789463 2790665 + RNA pseudouridine synthase family protein False
DVU3052 CDS 2796078 chromosome 3176887 3178866 - ABC transporter ATP-binding protein False
DVU3066 CDS 2796417 chromosome 3202265 3202834 - DNA-binding protein True
DVU3258 murA CDS 2793861 chromosome 3432618 3433871 - UDP-N-acetylglucosamine 1-carboxyvinyltransferase False
DVU3279 cobT CDS 2796003 chromosome 3454215 3455288 + nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 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.