Organism : Halobacterium salinarum NRC-1 | Module List :
VNG6176G kdpA

potassium-transporting ATPase subunit A

CircVis
Functional Annotations (6)
Function System
K+-transporting ATPase, A chain cog/ cog
potassium ion transport go/ biological_process
potassium-transporting ATPase activity go/ molecular_function
integral to membrane go/ cellular_component
Two-component system kegg/ kegg pathway
kdpA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG6176G
(Mouseover regulator name to see its description)

VNG6176G is regulated by 68 influences and regulates 0 modules.
Regulators for VNG6176G kdpA (68)
Regulator Module Operator
VNG1237C 5 tf
VNG1548C 5 tf
VNG2112C 5 tf
VNG1179C 15 tf
VNG1237C 15 tf
VNG6143H 15 tf
VNG1179C 18 tf
VNG1786H 18 tf
VNG2112C 18 tf
VNG6143H 18 tf
VNG1548C 31 tf
VNG2112C 31 tf
VNG6389G 31 tf
VNG6438G
VNG6288C
31 combiner
VNG1510C 26 tf
VNG1548C 26 tf
VNG6389G 26 tf
VNG2112C 62 tf
VNG2579G 62 tf
VNG6143H 62 tf
VNG6389G 62 tf
VNG2112C 28 tf
VNG6143H 28 tf
VNG1179C 21 tf
VNG1237C 21 tf
VNG1548C 21 tf
VNG2112C 21 tf
VNG6143H 21 tf
VNG6438G 21 tf
VNG0835G
VNG1451C
63 combiner
VNG1237C 63 tf
VNG1390H 63 tf
VNG2112C 63 tf
VNG6143H 63 tf
VNG1237C 53 tf
VNG2112C 53 tf
VNG6143H 53 tf
VNG1179C 47 tf
VNG1548C 47 tf
VNG6143H 47 tf
VNG6438G 47 tf
VNG0835G
VNG1451C
51 combiner
VNG1215G
VNG1548C
51 combiner
VNG1390H 51 tf
VNG1617H 51 tf
VNG6143H 51 tf
VNG6239G 51 tf
VNG6287H 51 tf
VNG1179C 70 tf
VNG6143H 70 tf
VNG0835G
VNG1451C
72 combiner
VNG1786H 72 tf
VNG6389G 72 tf
VNG6143H 177 tf
VNG6239G 177 tf
VNG6438G 177 tf
VNG1510C 74 tf
VNG1786H 74 tf
VNG2112C 74 tf
VNG6143H 74 tf
VNG6438G 74 tf
VNG1237C 279 tf
VNG1510C 279 tf
VNG6143H 279 tf
VNG1179C 69 tf
VNG1548C 69 tf
VNG6143H 69 tf
VNG6389G 69 tf

Warning: VNG6176G Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 34 motifs predicted.

Motif Table (34)
Motif Id e-value Consensus Motif Logo
989 1.10e+02 aAAtatAaaa.agga.taat
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990 8.30e+02 cgtccgCGA.tcG.t
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1009 1.40e-04 AAATatAAAtaAgat
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1010 2.50e-03 AaGtctAtTttgAGtgAAtGggA
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1015 0.00e+00 AccAttcaC.caaActacacata
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1016 0.00e+00 Aactgatt.AaAtctaAaaaagta
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1021 1.40e+02 Tt.t.actgTtTgtc
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1022 8.40e+02 cGTaCt.GACG
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1029 2.30e-02 gtTtcAgcaccGgcTctGaATagA
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1030 6.00e-03 atACtcttACaaagATAAAgaaGg
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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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1039 2.20e-03 gAcAtc.A..AacaA
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1040 7.70e+02 aATATAAa
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1071 7.70e-02 AcTcc.a.a.a.aTaa.TaA.ga
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1072 3.30e+02 AC.aaccTCaG
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1081 1.00e-01 gtcctCGaCGcgctcCTcGc.Gt
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1082 2.50e-01 CGtc.gCgAC.gCGa
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1099 1.70e-03 tGattttatCActgagaTaTtTgT
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1100 2.60e+02 cga.gacGtTctcAc
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1101 1.40e+03 ATacTCCGACAAaT
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1102 2.00e+03 GCaGTAGtG
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1113 4.20e-01 aaatta.tTAtcatt
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1114 2.30e+03 ATCGtT
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1115 1.70e+02 TGTTCA
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1116 3.20e+02 aCattCActAtTa
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1119 6.30e+01 CAT..tccgAcaaatacg.A
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1120 6.70e+01 TCGaTgtgtTCgT
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1123 8.80e+00 aCaatAttCa..Ca.At.aca
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1124 2.10e+03 gAagCagTagt
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1313 3.50e+01 AAATATAAA
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1314 4.60e+01 AGAAA.CaTC
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1487 1.10e+02 AGAgAA
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1488 1.40e+02 aac.cgT.c.AATCgg.gaa
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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 VNG6176G

VNG6176G is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
K+-transporting ATPase, A chain cog/ cog
potassium ion transport go/ biological_process
potassium-transporting ATPase activity go/ molecular_function
integral to membrane go/ cellular_component
Two-component system kegg/ kegg pathway
kdpA tigr/ tigrfam
Module neighborhood information for VNG6176G

VNG6176G has total of 143 gene neighbors in modules 5, 15, 18, 21, 26, 28, 31, 47, 51, 53, 62, 63, 69, 70, 72, 74, 177, 279
Gene neighbors (143)
Gene Common Name Description Module membership
VNG0027H hypothetical protein VNG0027H 26, 31, 72, 232, 243
VNG0034H hypothetical protein VNG0034H 28, 83
VNG0054H hypothetical protein VNG0054H 70, 111, 138, 147
VNG0057H hypothetical protein VNG0057H 26, 254
VNG0064G graD3 glucose-1-phosphate thymidylyltransferase 74, 164, 280, 293
VNG0076H hypothetical protein VNG0076H 28, 254
VNG0079H hypothetical protein VNG0079H 70, 111
VNG0081G moaE putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE 70, 111
VNG0117H hypothetical protein VNG0117H 72, 207, 209, 243, 298
VNG0139H hypothetical protein VNG0139H 17, 18, 30, 196
VNG0140H hypothetical protein VNG0140H 18, 26, 30, 239
VNG0157G oxlT oxalate/formate antiporter 53, 265
VNG0216H hypothetical protein VNG0216H 4, 13, 15, 20, 32, 43, 92, 93, 94, 103, 104, 105
VNG0217H hypothetical protein VNG0217H 13, 15, 20, 32, 43, 53, 92, 93, 94, 103, 105
VNG0357H hypothetical protein VNG0357H 70
VNG0396C hypothetical protein VNG0396C 26, 57, 243
VNG0512G ppe DNA double-strand break repair protein 18, 121, 177, 196
VNG0532H hypothetical protein VNG0532H 30, 70, 108
VNG0573C hypothetical protein VNG0573C 4, 5, 26, 28
VNG0596H hypothetical protein VNG0596H 53
VNG0612H hypothetical protein VNG0612H 26, 243
VNG0731H hypothetical protein VNG0731H 43, 53, 164
VNG0825C hypothetical protein VNG0825C 4, 5, 32, 43
VNG0869G tfbD transcription initiation factor IIB 18, 91, 95, 212
VNG0883H hypothetical protein VNG0883H 5, 26
VNG0979H hypothetical protein VNG0979H 70
VNG0985H hypothetical protein VNG0985H 4, 5, 164
VNG1000H hypothetical protein VNG1000H 20, 26, 31, 232
VNG1041H hypothetical protein VNG1041H 28
VNG1050H hypothetical protein VNG1050H 28, 53, 60
VNG1270H hypothetical protein VNG1270H 18, 30, 37, 42
VNG1271H hypothetical protein VNG1271H 18, 30, 37
VNG1299C hypothetical protein VNG1299C 53, 285
VNG1429C 2-phospho-L-lactate transferase 31, 232, 243
VNG1453H hypothetical protein VNG1453H 4, 28
VNG1455H hypothetical protein VNG1455H 26, 31, 57, 86
VNG1457C hypothetical protein VNG1457C 5
VNG1520G mutY A/G specific adenine glycosylase, repair protein 4, 5, 53
VNG1548C hypothetical protein VNG1548C 28, 293
VNG1577C hypothetical protein VNG1577C 20, 53, 96, 140, 173
VNG1580H hypothetical protein VNG1580H 20, 53, 140, 173, 277
VNG1582G hisC2 hypothetical protein VNG1582G 20, 53, 96, 140, 173
VNG1589C hypothetical protein VNG1589C 4, 5, 8, 28, 69, 85, 204
VNG1622G rfcB replication factor C large subunit 5, 28, 53, 140
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
VNG1781C hypothetical protein VNG1781C 21, 53, 60
VNG1783H hypothetical protein VNG1783H 53
VNG1784C DNA primase 28, 42, 68, 83, 234
VNG1890H hypothetical protein VNG1890H 18, 105, 167
VNG1902H hypothetical protein VNG1902H 53
VNG1918C geranylgeranylglyceryl phosphate synthase-like protein 13, 20, 53, 60
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
VNG1954H hypothetical protein VNG1954H 74
VNG1956H hypothetical protein VNG1956H 18, 30, 34, 42, 80, 91, 108, 115, 121
VNG1959G tgtA1 7-cyano-7-deazaguanine tRNA-ribosyltransferase 53, 129, 130, 132, 133
VNG1964H hypothetical protein VNG1964H 28, 63
VNG1976H hypothetical protein VNG1976H 26, 31, 60
VNG1986C hypothetical protein VNG1986C 17, 26, 30, 31, 108
VNG2002H hypothetical protein VNG2002H 26, 232
VNG2096G cctB thermosome subunit beta 4, 5, 28, 53, 140, 173
VNG2100G iluA threonine dehydratase 5, 20, 26, 28
VNG2108G thrC3 threonine synthase 28
VNG2214G dinF DNA damage-inducible protein 53, 60, 173
VNG2242C hypothetical protein VNG2242C 53
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
VNG2579G idr1 iron-dependent repressor-like protein 21
VNG2586C F420-0--gamma-glutamyl ligase 53, 206
VNG2678H hypothetical protein VNG2678H 28
VNG5047H None 15, 18, 63
VNG5112H None 117, 279
VNG5120H None 18, 37, 198
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
VNG6145H hypothetical protein VNG6145H 31, 72, 86, 106, 232, 298
VNG6152H hypothetical protein VNG6152H 4, 13, 15, 26, 31, 37, 142, 189, 272, 281, 297
VNG6157H hypothetical protein VNG6157H 18
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
VNG6179G cat3 cationic amino acid transporter 62, 72
VNG6183C hypothetical protein VNG6183C 15, 18, 213
VNG6184G cat4 cationic amino acid transporter 15, 18, 213
VNG6185H hypothetical protein VNG6185H 15, 18, 213
VNG6186H hypothetical protein VNG6186H 15, 18, 213
VNG6198H hypothetical protein VNG6198H 31
VNG6224H hypothetical protein VNG6224H 18, 91
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
VNG6233G gvpI2 GvpI protein, cluster B 31, 141, 188
VNG6235G gvpH2 GvpH protein, cluster B 31, 42, 141, 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
VNG6266H hypothetical protein VNG6266H 31, 146
VNG6292C hypothetical protein VNG6292C 17, 18, 30, 89
VNG6306C hypothetical protein VNG6306C 28
VNG6330H hypothetical protein VNG6330H 62, 112
VNG6339H hypothetical protein VNG6339H 26, 31, 69, 86, 106, 204, 232
VNG6340H hypothetical protein VNG6340H 62, 92, 93, 94, 96, 102, 103, 104
VNG6343H hypothetical protein VNG6343H 47, 69, 85
VNG6364H hypothetical protein VNG6364H 31, 106
VNG6366H hypothetical protein VNG6366H 62
VNG6367H hypothetical protein VNG6367H 47, 142
VNG6368H hypothetical protein VNG6368H 116, 272, 279
VNG6371G mrr Mrr restriction system protein-like protein 47, 272, 279
VNG6378H hypothetical protein VNG6378H 13, 21, 53, 60, 121, 189, 281
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
VNG6411H hypothetical protein VNG6411H 21, 277
VNG6416H hypothetical protein VNG6416H 13, 15, 21, 41, 60, 281
VNG6418H hypothetical protein VNG6418H 13, 18, 21, 41, 60, 281
VNG6419H hypothetical protein VNG6419H 13, 21, 60, 281
VNG6424H hypothetical protein VNG6424H 13, 15, 189
VNG6427H hypothetical protein VNG6427H 17, 18, 30, 62, 74, 89, 107
VNG6431H hypothetical protein VNG6431H 17, 26, 30, 38, 178
VNG6432H hypothetical protein VNG6432H 17, 26, 31, 38, 106, 243
VNG6439H hypothetical protein VNG6439H 26, 31, 243
VNG7011 repH plasmid replication protein RepH 17, 18, 30, 107, 122, 224, 287
VNG7044 hypothetical protein VNG7044 47, 153, 207
VNG7074 hypothetical protein VNG7074 135, 256, 279, 292
VNG7075 hypothetical protein VNG7075 87, 250, 279, 292
VNG7076 hypothetical protein VNG7076 252, 256, 276, 279
VNG7077 hypothetical protein VNG7077 87, 250, 276, 279
VNG7109 hypothetical protein VNG7109 4, 18, 38, 91
VNG7110 hypothetical protein VNG7110 18, 38, 91, 147
VNG7128 hypothetical protein VNG7128 21, 60, 281
VNG7136 hypothetical protein VNG7136 70, 138
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 VNG6176G
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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