Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0339

D-isomer specific 2-hydroxyacid dehydrogenase family protein

CircVis
Functional Annotations (8)
Function System
Lactate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
NAD binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0339
(Mouseover regulator name to see its description)

DVU0339 is regulated by 24 influences and regulates 0 modules.
Regulators for DVU0339 (24)
Regulator Module Operator
DVU0030 139 tf
DVU0230 139 tf
DVU0277
DVU0679
139 combiner
DVU0277
DVU3305
139 combiner
DVU1759 139 tf
DVU2036 139 tf
DVU2378 139 tf
DVU2567
DVU3313
139 combiner
DVU2989 139 tf
DVU3313 139 tf
DVU0277
DVU0309
81 combiner
DVU0277
DVU0744
81 combiner
DVU1759 81 tf
DVU2036 81 tf
DVU2036
DVU0110
81 combiner
DVU2036
DVU0569
81 combiner
DVU2378 81 tf
DVU2675 81 tf
DVU2960
DVU0569
81 combiner
DVU3023 81 tf
DVU3255
DVU0569
81 combiner
DVU3313 81 tf
DVU3313
DVU1063
81 combiner
DVU3313
DVU1156
81 combiner

Warning: DVU0339 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
159 1.90e-01 CAtAcgGCagGaCaG
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RegPredict
160 3.60e+01 tGCcCCCGgtaGCagTcCCgC
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RegPredict
269 3.90e-01 aACCttcaTcaatGaaaAGtTaCa
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RegPredict
270 3.00e+01 TgcatgccgaAgtTCGTc.gG.GT
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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 DVU0339

DVU0339 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Lactate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
metabolic process go/ biological_process
NAD binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for DVU0339

DVU0339 has total of 56 gene neighbors in modules 81, 139
Gene neighbors (56)
Gene Common Name Description Module membership
DVU0027 hypothetical protein DVU0027 81, 139
DVU0095 polyamine ABC transporter periplasmic polyamine-binding protein 139, 262
DVU0096 potC spermidine/putrescine ABC transporter membrane protein 139, 262
DVU0097 potB polyamine ABC transporter permease 81, 206
DVU0296 M24 family peptidase 81, 176
DVU0336 aminotransferase 81, 327
DVU0337 hypothetical protein DVU0337 81, 250
DVU0339 D-isomer specific 2-hydroxyacid dehydrogenase family protein 81, 139
DVU0340 acetyltransferase 81, 327
DVU0342 NAD-dependent epimerase/dehydratase family protein 81, 250
DVU0343 HPCH/HPAI aldolase family protein 81, 250
DVU0344 methyl-accepting chemotaxis protein 81, 103
DVU0432 ech hydrogenase subunit EchC 68, 139
DVU0493 hypothetical protein DVU0493 139, 175
DVU0953 tyrS tyrosyl-tRNA synthetase 139, 230
DVU1390 hypothetical protein DVU1390 139, 254
DVU1411 thiC thiamine biosynthesis protein ThiC 139, 306
DVU1530 metallo-beta-lactamase family protein 12, 139
DVU1539 glpX fructose 1,6-bisphosphatase II 139, 228
DVU1608 ligA DNA ligase, NAD-dependent 139, 166
DVU1609 dapB dihydrodipicolinate reductase 81, 176
DVU1912 hypothetical protein DVU1912 81, 262
DVU1917 hysB periplasmic 139, 348
DVU1918 hysA periplasmic 139, 348
DVU2347 argD acetylornithine aminotransferase 139, 262
DVU2370 outer membrane protein OmpH 81, 137
DVU2447 hypothetical protein DVU2447 33, 81
DVU2448 panC pantoate--beta-alanine ligase 81, 206
DVU2449 metK S-adenosylmethionine synthetase 81, 206
DVU2530 tkt transketolase 81, 250
DVU2683 L-lactate permease family protein 139, 166
DVU2790 hypothetical protein DVU2790 89, 139
DVU2791 cytochrome c family protein 139, 146
DVU2792 electron transport complex protein RnfC 139, 262
DVU2793 electron transport complex protein RnfD 139, 262
DVU2794 electron transport complex protein RnfG 139, 262
DVU2795 electron transport complex RsxE subunit 139, 262
DVU2796 electron transport complex protein RnfA 139, 262
DVU2797 ferredoxin 139, 315
DVU2798 ApbE family protein 139, 262
DVU2898 hypothetical protein DVU2898 81, 150
DVU2947 anaerobic ribonucleoside triphosphate reductase 81, 304
DVU3026 L-lactate permease family protein 139, 220
DVU3028 iron-sulfur cluster-binding protein 139, 220
DVU3033 iron-sulfur cluster-binding protein 139, 220
DVU3065 AMP-binding protein 81, 323
DVU3101 tonB protein 44, 139
DVU3119 AMP-binding protein 81, 230
DVU3181 purL phosphoribosylformylglycinamidine synthase II 81, 174
DVU3233 flhB flagellar biosynthesis protein FlhB 81, 334
DVU3234 flagellar biosynthetic protein FliR 81, 286
DVU3235 IMP cyclohydrolase 81, 220
DVU3347 pyruvate ferredoxin/flavodoxin oxidoreductase family protein 81, 220
DVU3371 metE 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 81, 139
DVU3373 ilvD dihydroxy-acid dehydratase 81, 250
DVU3374 permease 81, 250
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 DVU0339
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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