Organism : Halobacterium salinarum NRC-1 | Module List :
VNG1648G trpF

hypothetical protein VNG1648G

CircVis
Functional Annotations (6)
Function System
Phosphoribosylanthranilate isomerase cog/ cog
phosphoribosylanthranilate isomerase activity go/ molecular_function
tryptophan metabolic process go/ biological_process
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG1648G
(Mouseover regulator name to see its description)

VNG1648G is regulated by 29 influences and regulates 0 modules.
Regulators for VNG1648G trpF (29)
Regulator Module Operator
VNG1237C 5 tf
VNG1548C 5 tf
VNG2112C 5 tf
VNG1237C 4 tf
VNG2112C 4 tf
VNG6143H 4 tf
VNG2112C 28 tf
VNG6143H 28 tf
VNG1179C 48 tf
VNG1237C 48 tf
VNG1510C 48 tf
VNG1786H 48 tf
VNG2112C 48 tf
VNG2579G 48 tf
VNG0869G 87 tf
VNG1179C 87 tf
VNG2579G 87 tf
VNG5163G 87 tf
VNG6438G 87 tf
VNG1179C 30 tf
VNG1237C 30 tf
VNG1786H 30 tf
VNG2112C 30 tf
VNG6143H 30 tf
VNG6438G 30 tf
VNG1179C 64 tf
VNG1786H 64 tf
VNG6143H 64 tf
VNG6438G 64 tf

Warning: VNG1648G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 14 motifs predicted.

Motif Table (14)
Motif Id e-value Consensus Motif Logo
987 3.00e-03 aAaAc.Acg.cCtagctaaaatAa
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988 8.90e-01 GtCTTggGCGAaTaGAAAtCTTCt
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989 1.10e+02 aAAtatAaaa.agga.taat
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990 8.30e+02 cgtccgCGA.tcG.t
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1033 9.50e+01 CGA.Cacgtcg.tgacgctcA
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1034 1.30e+03 t.A.tgaatTAcGGa
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1037 1.10e-03 aAaagaAAT.tTCTctTCAcgaat
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1038 1.90e-03 taCgagacaa.gccgacatt.act
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1073 5.80e-01 acTgT.cgAg.CtgT.cG
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1074 2.20e+02 AACGCAAATCCTTA
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1103 1.90e+02 acta.ac.ct..caT.ActTa
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1104 1.80e+03 GTtccGgaTcgCcG.c
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1149 1.40e-02 TaggtttTaaGt.aaCat
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1150 1.40e+01 acaa.aTGtCCGcTa
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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 VNG1648G

VNG1648G is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Phosphoribosylanthranilate isomerase cog/ cog
phosphoribosylanthranilate isomerase activity go/ molecular_function
tryptophan metabolic process go/ biological_process
Phenylalanine tyrosine and tryptophan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for VNG1648G

VNG1648G has total of 91 gene neighbors in modules 4, 5, 28, 30, 48, 64, 87
Gene neighbors (91)
Gene Common Name Description Module membership
VNG0020H hypothetical protein VNG0020H 30, 108, 247
VNG0022H hypothetical protein VNG0022H 30, 254
VNG0023H hypothetical protein VNG0023H 30, 254, 290
VNG0034H hypothetical protein VNG0034H 28, 83
VNG0076H hypothetical protein VNG0076H 28, 254
VNG0139H hypothetical protein VNG0139H 17, 18, 30, 196
VNG0140H hypothetical protein VNG0140H 18, 26, 30, 239
VNG0196H hypothetical protein VNG0196H 30, 267, 281
VNG0216H hypothetical protein VNG0216H 4, 13, 15, 20, 32, 43, 92, 93, 94, 103, 104, 105
VNG0469H hypothetical protein VNG0469H 30, 91
VNG0470G trp3 daunorubicin resistance ABC transporter ATP-binding protein 30, 91
VNG0532H hypothetical protein VNG0532H 30, 70, 108
VNG0573C hypothetical protein VNG0573C 4, 5, 26, 28
VNG0811H hypothetical protein VNG0811H 30, 87, 138, 147
VNG0813G potD spermidine/putrescine-binding protein 87, 138, 147
VNG0825C hypothetical protein VNG0825C 4, 5, 32, 43
VNG0883H hypothetical protein VNG0883H 5, 26
VNG0926H hypothetical protein VNG0926H 30, 108
VNG0985H hypothetical protein VNG0985H 4, 5, 164
VNG1041H hypothetical protein VNG1041H 28
VNG1050H hypothetical protein VNG1050H 28, 53, 60
VNG1059C hypothetical protein VNG1059C 87, 213
VNG1060H hypothetical protein VNG1060H 87, 213
VNG1270H hypothetical protein VNG1270H 18, 30, 37, 42
VNG1271H hypothetical protein VNG1271H 18, 30, 37
VNG1453H hypothetical protein VNG1453H 4, 28
VNG1457C hypothetical protein VNG1457C 5
VNG1520G mutY A/G specific adenine glycosylase, repair protein 4, 5, 53
VNG1548C hypothetical protein VNG1548C 28, 293
VNG1589C hypothetical protein VNG1589C 4, 5, 8, 28, 69, 85, 204
VNG1622G rfcB replication factor C large subunit 5, 28, 53, 140
VNG1646G trpG1 anthranilate synthase subunit beta 30, 48, 64, 87
VNG1647G trpE1 anthranilate synthase component I 48, 64
VNG1648G trpF hypothetical protein VNG1648G 4, 5, 28, 30, 48, 64, 87
VNG1649G trpD anthranilate phosphoribosyltransferase 28, 30, 48, 64, 87, 92
VNG1650H hypothetical protein VNG1650H 4, 5, 30, 34, 35, 245, 295
VNG1681C hypothetical protein VNG1681C 20, 26, 28, 31, 147, 232
VNG1733G htr17 Htr17 64, 74
VNG1734H hypothetical protein VNG1734H 64, 74
VNG1784C DNA primase 28, 42, 68, 83, 234
VNG1831H hypothetical protein VNG1831H 64
VNG1952H hypothetical protein VNG1952H 18, 28, 30, 42, 68, 80, 91, 108, 121, 135
VNG1953C hypothetical protein VNG1953C 13, 18, 30, 34, 42, 80, 91, 108, 115, 121
VNG1956H hypothetical protein VNG1956H 18, 30, 34, 42, 80, 91, 108, 115, 121
VNG1964H hypothetical protein VNG1964H 28, 63
VNG1986C hypothetical protein VNG1986C 17, 26, 30, 31, 108
VNG2096G cctB thermosome subunit beta 4, 5, 28, 53, 140, 173
VNG2100G iluA threonine dehydratase 5, 20, 26, 28
VNG2108G thrC3 threonine synthase 28
VNG2230H hypothetical protein VNG2230H 64
VNG2231C hypothetical protein VNG2231C 64
VNG2316C hypothetical protein VNG2316C 48, 178
VNG2317G cbiO1 cobalt transport ATP-binding protein 38, 48, 178
VNG2386C hypothetical protein VNG2386C 13, 28
VNG2414H hypothetical protein VNG2414H 18, 38, 64
VNG2444C hypothetical protein VNG2444C 17, 28, 31, 38, 173
VNG2466C None 13, 31, 64, 70, 166
VNG2474C hypothetical protein VNG2474C 48, 279
VNG2475C hypothetical protein VNG2475C 48, 256, 279
VNG2563H hypothetical protein VNG2563H 48, 58
VNG2565G trkH3 TRK potassium uptake system protein 48, 58
VNG2678H hypothetical protein VNG2678H 28
VNG6143H hypothetical protein VNG6143H 5, 26, 31, 72, 86, 106, 204, 232, 243, 295, 298
VNG6144G trsE transfer complex protein 4, 5, 42, 68, 295
VNG6150G orc1 orc / cell division control protein 6 4, 13, 38, 142, 189
VNG6152H hypothetical protein VNG6152H 4, 13, 15, 26, 31, 37, 142, 189, 272, 281, 297
VNG6170H hypothetical protein VNG6170H 4, 5, 15, 26, 28, 31, 36, 53, 60, 63, 69, 72, 85, 122
VNG6175G trkA2 TRK potassium uptake system protein 5, 15, 62, 69, 72, 177
VNG6176G kdpA potassium-transporting ATPase subunit A 5, 15, 18, 21, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279
VNG6177G kdpB potassium-transporting ATPase subunit B 5, 15, 62, 63, 69, 72
VNG6178G kdpC potassium-transporting ATPase C chain 5, 15, 18, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279
VNG6191H hypothetical protein VNG6191H 17, 30, 34, 38, 41, 44, 80, 91
VNG6196G phoT2 sodium-dependent phosphate transporter 30, 36, 41, 80, 87, 89
VNG6230G gvpK2 GvpK protein, cluster B 4, 5, 8, 22, 28, 31, 141, 148, 181, 182, 188, 200
VNG6232G gvpJ2 GvpJ protein, cluster B 4, 5, 8, 28, 31, 42, 141, 148, 182, 188
VNG6236G gvpG2 GvpG protein, cluster B 8, 28, 141, 148, 181, 182, 188
VNG6239G gvpE2 GvpE protein, cluster B 4, 5, 8, 28, 141, 148, 182, 188, 200
VNG6244G gvpN2 GvpN protein, cluster B 5, 26, 53, 185
VNG6258C hypothetical protein VNG6258C 18, 30, 108
VNG6292C hypothetical protein VNG6292C 17, 18, 30, 89
VNG6306C hypothetical protein VNG6306C 28
VNG6390H hypothetical protein VNG6390H 4, 26, 30, 34, 35, 245, 295
VNG6400H hypothetical protein VNG6400H 18, 30, 80, 133, 245, 290
VNG6404H hypothetical protein VNG6404H 28, 69
VNG6406H hypothetical protein VNG6406H 5, 127
VNG6427H hypothetical protein VNG6427H 17, 18, 30, 62, 74, 89, 107
VNG6431H hypothetical protein VNG6431H 17, 26, 30, 38, 178
VNG7011 repH plasmid replication protein RepH 17, 18, 30, 107, 122, 224, 287
VNG7075 hypothetical protein VNG7075 87, 250, 279, 292
VNG7077 hypothetical protein VNG7077 87, 250, 276, 279
VNG7109 hypothetical protein VNG7109 4, 18, 38, 91
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 VNG1648G
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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