Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0336

aminotransferase

CircVis
Functional Annotations (3)
Function System
Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis cog/ cog
catalytic activity go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0336
(Mouseover regulator name to see its description)

DVU0336 is regulated by 27 influences and regulates 0 modules.
Regulators for DVU0336 (27)
Regulator Module Operator
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
DVU0277
DVU0946
327 combiner
DVU0525 327 tf
DVU0653 327 tf
DVU1561
DVU3142
327 combiner
DVU1561
DVUA0057
327 combiner
DVU2036
DVU2114
327 combiner
DVU2832
DVU1745
327 combiner
DVU3023 327 tf
DVU3142 327 tf
DVU3255
DVU0594
327 combiner
DVU3255
DVU0653
327 combiner
DVU3255
DVU3193
327 combiner
DVUA0024 327 tf

Warning: DVU0336 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
Loader icon
RegPredict
160 3.60e+01 tGCcCCCGgtaGCagTcCCgC
Loader icon
RegPredict
621 9.20e+02 GgTTTTC
Loader icon
RegPredict
622 6.60e+00 G.AtCccggAAccg
Loader icon
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 DVU0336

DVU0336 is enriched for 3 functions in 3 categories.
Module neighborhood information for DVU0336

DVU0336 has total of 47 gene neighbors in modules 81, 327
Gene neighbors (47)
Gene Common Name Description Module membership
DVU0021 hypothetical protein DVU0021 206, 327
DVU0027 hypothetical protein DVU0027 81, 139
DVU0091 hypothetical protein DVU0091 9, 327
DVU0097 potB polyamine ABC transporter permease 81, 206
DVU0296 M24 family peptidase 81, 176
DVU0327 exopolysaccharide biosynthesis protein 48, 327
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
DVU0451 chloride channel family protein 75, 327
DVU1056 cobalt ABC transporter ATP-binding protein 33, 327
DVU1276 hypothetical protein DVU1276 154, 327
DVU1347 M24/M37 family peptidase 33, 327
DVU1609 dapB dihydrodipicolinate reductase 81, 176
DVU1611 molybdopterin oxidoreductase domain-containing protein 48, 327
DVU1772 pyridine nucleotide-disulfide oxidoreductase 250, 327
DVU1912 hypothetical protein DVU1912 81, 262
DVU2367 lpxA UDP-N-acetylglucosamine acyltransferase 154, 327
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
DVU2558 bioB biotin synthase 9, 327
DVU2757 radical SAM domain-containing protein 180, 327
DVU2898 hypothetical protein DVU2898 81, 150
DVU2942 purB adenylosuccinate lyase 180, 327
DVU2947 anaerobic ribonucleoside triphosphate reductase 81, 304
DVU3065 AMP-binding protein 81, 323
DVU3119 AMP-binding protein 81, 230
DVU3167 heme biosynthesis protein 180, 327
DVU3168 hemL glutamate-1-semialdehyde aminotransferase 23, 327
DVU3174 ubiE ubiquinone/menaquinone biosynthesis methlytransferase UbiE 164, 327
DVU3175 hypothetical protein DVU3175 33, 327
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
DVU3239 PAP2 family protein 126, 327
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 DVU0336
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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