Organism : Desulfovibrio vulgaris Hildenborough | Module List:
Module 150 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 150

There are 15 regulatory influences for Module 150

Regulator Table (15)
Regulator Name Type
DVU1063 tf
DVU1572
DVU0230
combiner
DVUA0151 tf
DVU0653
DVU1156
combiner
DVU0653
DVUA0100
combiner
DVU1674 tf
DVU3023
DVU0569
combiner
DVU0744
DVU0569
combiner
DVU3167
DVUA0100
combiner
DVU0569 tf
DVU0653
DVU2934
combiner
DVU0653
DVU0744
combiner
DVU1964
DVU1063
combiner
DVU0619
DVU0569
combiner
DVU1674
DVU0525
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
285 3.90e+00 ccATCatC
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RegPredict
286 1.30e+02 GctGCGCAgtCaGgCgGC
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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 150 is enriched for following functions.

KEGG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini Hochberg pvalue Genes with function Method
Metabolic pathways kegg pathway 7.47e-03 1.49e-02 8/29
Carbohydrate Metabolism kegg subcategory 1.05e-03 7.58e-03 6/29
Metabolism kegg subcategory 1.05e-02 3.67e-02 11/29
Metabolism kegg category 2.96e-03 1.95e-02 13/29
Metabolism kegg category 2.12e-02 4.40e-02 8/29
Carbohydrate Metabolism kegg subcategory 1.86e-02 4.02e-02 3/29
Global kegg category 8.77e-03 2.42e-02 8/29
Metabolism kegg subcategory 8.77e-03 2.42e-02 8/29
Metabolic pathways kegg pathway 7.47e-03 2.20e-02 8/29

GO Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
metabolic process biological_process 3.46e-03 6.37e-03 4/29
DNA-directed DNA polymerase activity molecular_function 0.00e+00 0.00e+00 14/29
protein serine/threonine phosphatase activity molecular_function 0.00e+00 0.00e+00 3/29

TIGRFam Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Other tigr sub1role 0.00e+00 3.00e-06 3/29
Mobile and extrachromosomal element functions tigr mainrole 1.50e-04 2.35e-03 3/29
Mobile and extrachromosomal element functions tigr mainrole 1.50e-04 3.37e-04 3/29
Other tigr sub1role 0.00e+00 0.00e+00 3/29

COG Enrichment Table

Function Name Function Type Unadjusted pvalue Benjamini& Hochberg pvalue Genes with function Method
Replication, recombination and repair cog subcategory 8.38e-03 1.47e-02 3/29
Coenzyme transport and metabolism cog subcategory 1.58e-02 2.62e-02 3/29
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 150

There are 29 genes in Module 150

Gene Member Table (29)
Name Common name Type Gene ID Chromosome Start End Strand Description TF
DVU0478 CDS 2793623 chromosome 543608 544471 + serine/threonine protein phosphatase family protein False
DVU0489 paaK-1 CDS 2793703 chromosome 556585 557883 + phenylacetate-coenzyme A ligase False
DVU0571 ald CDS 2793416 chromosome 636374 637486 + alanine dehydrogenase False
DVU0615 CDS 2794401 chromosome 683330 683494 + hypothetical protein DVU0615 False
DVU0632 CDS 2794554 chromosome 699063 699680 - cupin family protein False
DVU0748 acs CDS 2794966 chromosome 837106 839052 - acetyl-CoA synthetase False
DVU0767 CDS 2795571 chromosome 857778 858884 - class V aminotransferase False
DVU0768 murI CDS 2795572 chromosome 858973 859821 - glutamate racemase False
DVU0769 CDS 2794840 chromosome 859823 860701 - pyridoxamine kinase False
DVU1252 CDS 2794598 chromosome 1337944 1340220 + hypothetical protein DVU1252 False
DVU1797 ksgA CDS 2796706 chromosome 1858413 1859288 - dimethyladenosine transferase False
DVU1908 pdxJ CDS 2793681 chromosome 1983729 1984454 + pyridoxine 5'-phosphate synthase False
DVU1944 CDS 2793516 chromosome 2017637 2017909 + pyruvate ferredoxin oxidoreductase, iron-sulfur binding subunit False
DVU2620 CDS 2795237 chromosome 2740315 2741475 + hypothetical protein DVU2620 False
DVU2898 CDS 2793928 chromosome 2996736 2997737 + hypothetical protein DVU2898 False
DVU2995 CDS 2796309 chromosome 3105499 3106662 - glycosyl transferase group 1 family protein False
DVU2996 CDS 2796310 chromosome 3106817 3107740 - NAD-dependent epimerase/dehydratase family protein False
DVU2997 CDS 2796311 chromosome 3107742 3108518 - hypothetical protein DVU2997 False
DVU2998 CDS 2796312 chromosome 3108548 3109882 - hypothetical protein DVU2998 False
DVU3126 CDS 2796618 chromosome 3273316 3274547 + None False
DVU3287 CDS 2796011 chromosome 3461929 3463962 - glycosyl transferase group 2 family protein False
DVUA0061 CDS 2781510 pDV 75835 77187 + hypothetical protein DVUA0061 False
DVUA0098 CDS 2781506 pDV 132351 133400 - dehydrogenase False
DVUA0112 CDS 2781618 pDV 149369 151243 + type III secretion system protein YscC family False
DVUA0119 CDS 2781474 pDV 157639 158955 + type III secretion system ATPase False
DVUA0124 CDS 2781525 pDV 162643 163059 + sigma factor serine-protein kinase False
DVUA0132 CDS 2781595 pDV 172897 173769 + CRISPR-associated Csh2 family protein False
DVUA0134 cas1 CDS 2781520 pDV 174393 175424 + CRISPR-associated Cas1 family protein False
DVUA0135 CDS 2781581 pDV 175411 175719 + CRISPR-associated Cas2 family protein 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.