Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3208

membrane protein

CircVis
Functional Annotations (6)
Function System
Predicted membrane protein cog/ cog
glycerol-3-phosphate O-acyltransferase activity go/ molecular_function
Glycerolipid metabolism kegg/ kegg pathway
Glycerophospholipid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
TIGR00023 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3208
(Mouseover regulator name to see its description)

DVU3208 is regulated by 23 influences and regulates 0 modules.
Regulators for DVU3208 (23)
Regulator Module Operator
DVU0309
DVU0653
223 combiner
DVU0653 223 tf
DVU1561
DVU1964
223 combiner
DVU1788
DVU2275
223 combiner
DVU1949 223 tf
DVU2036
DVU2275
223 combiner
DVU2275 223 tf
DVU2557
DVU2195
223 combiner
DVU2909
DVU0653
223 combiner
DVU2909
DVU2275
223 combiner
DVU3167 223 tf
DVU0110 62 tf
DVU0309
DVU1340
62 combiner
DVU0309
DVU1547
62 combiner
DVU0309
DVU3023
62 combiner
DVU1517 62 tf
DVU1561
DVU1584
62 combiner
DVU2547
DVU1730
62 combiner
DVU2567
DVU2675
62 combiner
DVU2960
DVU1730
62 combiner
DVU3080 62 tf
DVU3167 62 tf
DVUA0024 62 tf

Warning: DVU3208 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
121 1.70e-05 aattt.atGCcAGCCcTA.AGT
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RegPredict
122 3.60e+00 atAcaAaGATcAtTTTaT
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RegPredict
425 1.20e-02 GggcgcAaGgC
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RegPredict
426 8.40e+03 gGCaTcGtATcgAcGaatCaC
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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 DVU3208

DVU3208 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Predicted membrane protein cog/ cog
glycerol-3-phosphate O-acyltransferase activity go/ molecular_function
Glycerolipid metabolism kegg/ kegg pathway
Glycerophospholipid metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
TIGR00023 tigr/ tigrfam
Module neighborhood information for DVU3208

DVU3208 has total of 54 gene neighbors in modules 62, 223
Gene neighbors (54)
Gene Common Name Description Module membership
DVU0135 hypothetical protein DVU0135 223, 278
DVU0136 hypothetical protein DVU0136 44, 223
DVU0141 M50 family peptidase 9, 223
DVU0247 response regulator 35, 62
DVU0250 hypothetical protein DVU0250 62, 280
DVU0319 NAD-dependent epimerase/dehydratase 62, 119
DVU0323 folD bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 9, 223
DVU0325 hypD hydrogenase expression/formation protein HypD 22, 62
DVU0349 NeuB family protein 62, 250
DVU0394 radical SAM domain-containing protein 62, 99
DVU0414 NADP-dependent malic enzyme-like protein 176, 223
DVU0499 hypothetical protein DVU0499 46, 62
DVU0523 flgM negative regulator of flagellin synthesis FlgM 62, 122
DVU0524 hypothetical protein DVU0524 62, 122
DVU0660 phosphodiesterase 223, 278
DVU0724 sodium/alanine symporter family protein 223, 278
DVU0726 tgt queuine tRNA-ribosyltransferase 176, 223
DVU0795 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 176, 223
DVU0796 hisD histidinol dehydrogenase 113, 223
DVU0800 hypothetical protein DVU0800 62, 225
DVU1029 hisC histidinol-phosphate aminotransferase 9, 223
DVU1060 glycosyl transferase group 1 family protein 223, 278
DVU1091 hypothetical protein DVU1091 57, 223
DVU1220 nitroreductase family protein 223, 323
DVU1540 purU formyltetrahydrofolate deformylase 9, 223
DVU1670 hypothetical protein DVU1670 53, 62
DVU1693 gltX-1 glutamyl-tRNA synthetase 223, 275
DVU1827 diaminopimelate aminotransferase 223, 258
DVU1868 dapA dihydrodipicolinate synthase 62, 236
DVU1942 DAK2 and DegV domain-containing protein 223, 228
DVU1953 proA gamma-glutamyl phosphate reductase 46, 62
DVU1978 Na+/H+ antiporter family protein 223, 294
DVU2042 Fic family protein 62, 273
DVU2055 metG methionyl-tRNA synthetase 30, 223
DVU2082 flagellin 62, 236
DVU2203 L-PSP family endoribonuclease 62, 236
DVU2210 hypothetical protein 180, 223
DVU2436 hypothetical protein DVU2436 223, 278
DVU2446 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase 62, 115
DVU2471 oxidoreductase, selenocysteine-containing 63, 223
DVU2475 ferredoxin-NADP(+) reductase subunit alpha 46, 62
DVU2493 iron-sulfur cluster-binding protein 185, 223
DVU2552 gltX glutamyl-tRNA synthetase 113, 223
DVU2735 paaK-3 phenylacetate-coenzyme A ligase 62, 236
DVU2756 radical SAM domain-containing protein 62, 278
DVU2883 selA selenocysteine synthase 62, 162
DVU2884 aminopeptidase 1 62, 222
DVU2892 GTP cyclohydrolase 180, 223
DVU2897 hypothetical protein DVU2897 62, 277
DVU2948 flagellin N-terminal domain-containing protein 62, 122
DVU3068 GAF domain/sensory box/EAL domain-containing protein 35, 62
DVU3208 membrane protein 62, 223
DVU3364 hypothetical protein DVU3364 35, 62
DVU3389 topA DNA topoisomerase I 223, 228
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 DVU3208
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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