Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0098

dehydrogenase

CircVis
Functional Annotations (9)
Function System
Glycerol dehydrogenase and related enzymes cog/ cog
3-dehydroquinate synthase activity go/ molecular_function
transporter activity go/ molecular_function
transport go/ biological_process
metabolic process go/ biological_process
aromatic amino acid family biosynthetic process go/ biological_process
membrane go/ cellular_component
metal ion binding go/ molecular_function
glycerol-1-phosphate dehydrogenase [NAD(P)+] activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0098
(Mouseover regulator name to see its description)

DVUA0098 is regulated by 23 influences and regulates 0 modules.
Regulators for DVUA0098 (23)
Regulator Module Operator
DVU0569 150 tf
DVU0619
DVU0569
150 combiner
DVU0653
DVU0744
150 combiner
DVU0653
DVU1156
150 combiner
DVU0653
DVU2934
150 combiner
DVU0653
DVUA0100
150 combiner
DVU0744
DVU0569
150 combiner
DVU1063 150 tf
DVU1572
DVU0230
150 combiner
DVU1674 150 tf
DVU1674
DVU0525
150 combiner
DVU1964
DVU1063
150 combiner
DVU3023
DVU0569
150 combiner
DVU3167
DVUA0100
150 combiner
DVUA0151 150 tf
DVU0309
DVU3381
266 combiner
DVU0744
DVU2690
266 combiner
DVU1745 266 tf
DVU2275 266 tf
DVU2802
DVU0057
266 combiner
DVU2802
DVU2319
266 combiner
DVU2802
DVU2588
266 combiner
DVU2802
DVU3334
266 combiner

Warning: DVUA0098 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
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
507 7.10e+01 AttttaTgctga.Att.aT..taa
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RegPredict
508 5.40e+02 A.gGCAAgcA
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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 for DVUA0098

DVUA0098 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Glycerol dehydrogenase and related enzymes cog/ cog
3-dehydroquinate synthase activity go/ molecular_function
transporter activity go/ molecular_function
transport go/ biological_process
metabolic process go/ biological_process
aromatic amino acid family biosynthetic process go/ biological_process
membrane go/ cellular_component
metal ion binding go/ molecular_function
glycerol-1-phosphate dehydrogenase [NAD(P)+] activity go/ molecular_function
Module neighborhood information for DVUA0098

DVUA0098 has total of 52 gene neighbors in modules 150, 266
Gene neighbors (52)
Gene Common Name Description Module membership
DVU0478 serine/threonine protein phosphatase family protein 14, 150
DVU0489 paaK-1 phenylacetate-coenzyme A ligase 150, 176
DVU0571 ald alanine dehydrogenase 150, 175
DVU0615 hypothetical protein DVU0615 150, 198
DVU0632 cupin family protein 150, 176
DVU0692 molybdopterin oxidoreductase, transmembrane subunit 74, 266
DVU0693 molybdopterin oxidoreductase, iron-sulfur cluster-binding subunit 74, 266
DVU0694 molybdopterin oxidoreductase, molybdopterin-binding subunit 74, 266
DVU0748 acs acetyl-CoA synthetase 150, 296
DVU0767 class V aminotransferase 150, 337
DVU0768 murI glutamate racemase 150, 278
DVU0769 pyridoxamine kinase 150, 278
DVU0834 rnhB ribonuclease HII 26, 266
DVU0912 hypothetical protein DVU0912 11, 266
DVU0917 atpE ATP synthase F0 subunit C 74, 266
DVU0919 hypothetical protein DVU0919 74, 266
DVU1109 ATPase 266, 331
DVU1121 hypothetical protein DVU1121 11, 266
DVU1235 hypothetical protein DVU1235 92, 266
DVU1252 hypothetical protein DVU1252 150, 250
DVU1264 transglycosylase 74, 266
DVU1296 hypothetical protein DVU1296 74, 266
DVU1751 hypothetical protein DVU1751 239, 266
DVU1794 hypothetical protein DVU1794 266, 297
DVU1795 hup-3 DNA-binding protein HU 266, 297
DVU1797 ksgA dimethyladenosine transferase 75, 150
DVU1902 hypothetical protein DVU1902 266, 285
DVU1908 pdxJ pyridoxine 5'-phosphate synthase 33, 150
DVU1932 adk adenylate kinase 74, 266
DVU1944 pyruvate ferredoxin oxidoreductase, iron-sulfur binding subunit 150, 337
DVU2002 hypothetical protein DVU2002 92, 266
DVU2033 hypothetical protein DVU2033 266, 344
DVU2102 OMP85 family outer membrane protein 92, 266
DVU2620 hypothetical protein DVU2620 150, 291
DVU2696 hypothetical protein DVU2696 266, 344
DVU2697 hypothetical protein DVU2697 266, 344
DVU2898 hypothetical protein DVU2898 81, 150
DVU2995 glycosyl transferase group 1 family protein 150, 278
DVU2996 NAD-dependent epimerase/dehydratase family protein 87, 150
DVU2997 hypothetical protein DVU2997 87, 150
DVU2998 hypothetical protein DVU2998 87, 150
DVU3126 None 87, 150
DVU3276 ferredoxin I 208, 266
DVU3287 glycosyl transferase group 2 family protein 46, 150
DVUA0061 hypothetical protein DVUA0061 53, 150
DVUA0098 dehydrogenase 150, 266
DVUA0112 type III secretion system protein YscC family 136, 150
DVUA0119 type III secretion system ATPase 136, 150
DVUA0124 sigma factor serine-protein kinase 136, 150
DVUA0132 CRISPR-associated Csh2 family protein 131, 150
DVUA0134 cas1 CRISPR-associated Cas1 family protein 150, 266
DVUA0135 CRISPR-associated Cas2 family protein 121, 150
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

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.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for DVUA0098
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend