Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0712

amino acid ABC transporter periplasmic-binding protein

CircVis
Functional Annotations (4)
Function System
ABC-type branched-chain amino acid transport systems, periplasmic component cog/ cog
amino acid transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0712
(Mouseover regulator name to see its description)

DVU0712 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU0712 (19)
Regulator Module Operator
DVU0277
DVU1690
262 combiner
DVU0277
DVU1745
262 combiner
DVU0525 262 tf
DVU0606
DVU2251
262 combiner
DVU0679
DVU2251
262 combiner
DVU2319
DVU2690
262 combiner
DVU2557
DVU0653
262 combiner
DVU2557
DVU0936
262 combiner
DVU3167
DVU2251
262 combiner
DVU3313 262 tf
DVU3313
DVU0230
262 combiner
DVU0309
DVU0539
331 combiner
DVU0936
DVU1584
331 combiner
DVU2106 331 tf
DVU2423 331 tf
DVU2802
DVU2989
331 combiner
DVU3080 331 tf
DVU3186 331 tf
DVUA0151
DVU1730
331 combiner

Warning: DVU0712 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
499 1.00e+02 TtGtgAAA
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RegPredict
500 9.80e+03 Aaa.tgtGCttTccCgcTcCaTt
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RegPredict
629 2.80e+00 aaaTGACtAaAAaGaGTaTaTA
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RegPredict
630 2.60e+00 CGTcaaTAtCaatCcAcAG.TtcC
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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 DVU0712

DVU0712 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type branched-chain amino acid transport systems, periplasmic component cog/ cog
amino acid transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for DVU0712

DVU0712 has total of 48 gene neighbors in modules 262, 331
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0073 CDP-glucose-4,6-dehydratase 331, 337
DVU0095 polyamine ABC transporter periplasmic polyamine-binding protein 139, 262
DVU0096 potC spermidine/putrescine ABC transporter membrane protein 139, 262
DVU0293 dksA/traR C4-type zinc finger family protein 251, 331
DVU0386 amino acid ABC transporter periplasmic amino acid-binding protein 262, 288
DVU0428 hypothetical protein DVU0428 14, 331
DVU0477 icd isocitrate dehydrogenase, NADP-dependent 230, 262
DVU0605 hypothetical protein DVU0605 92, 331
DVU0645 methyl-accepting chemotaxis protein 103, 331
DVU0712 amino acid ABC transporter periplasmic-binding protein 262, 331
DVU0714 branched-chain amino acid ABC transporter permease 331, 347
DVU0715 branched-chain amino acid ABC transporter ATP binding protein 215, 331
DVU0716 branched-chain amino acid ABC transporter ATP-binding protein 215, 331
DVU0875 fumarylacetoacetate hydrolase family protein 318, 331
DVU0902 hypothetical protein 175, 331
DVU0925 rfbA glucose-1-phosphate thymidylyltransferase 331, 332
DVU0937 hypothetical protein DVU0937 11, 262
DVU1014 hypothetical protein DVU1014 267, 331
DVU1095 argG argininosuccinate synthase 220, 262
DVU1108 hypothetical protein DVU1108 239, 331
DVU1109 ATPase 266, 331
DVU1479 hypothetical protein DVU1479 246, 331
DVU1661 hypothetical protein DVU1661 29, 331
DVU1746 C-5 cytosine-specific DNA methylase family protein 306, 331
DVU1777 cynT carbonic anhydrase 179, 262
DVU1833 phosphoenolpyruvate synthase 44, 331
DVU1837 competence protein 331, 332
DVU1912 hypothetical protein DVU1912 81, 262
DVU1934 phosphonate ABC transporter permease 33, 262
DVU1937 phosphonate ABC transporter periplasmic phosphonate-binding protein 145, 262
DVU2098 cooS carbon monoxide dehydrogenase 179, 262
DVU2205 tryptophan-specific transport protein 255, 262
DVU2342 amino acid ABC transporter periplasmic amino acid-binding protein 178, 262
DVU2347 argD acetylornithine aminotransferase 139, 262
DVU2348 dut deoxyuridine 5'-triphosphate nucleotidohydrolase 153, 262
DVU2364 class I/II aminotransferase 146, 262
DVU2452 hypothetical protein DVU2452 263, 331
DVU2529 pgk phosphoglycerate kinase 262, 296
DVU2617 sodium/calcium exchanger family protein 116, 331
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
DVU2798 ApbE family protein 139, 262
DVU2931 sensory box histidine kinase 75, 262
DVU3171 cytochrome c3 146, 262
DVU3288 hypothetical protein DVU3288 225, 331
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 DVU0712
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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