Organism : Halobacterium salinarum NRC-1 | Module List :
VNG6193H

hypothetical protein VNG6193H

CircVis
Functional Annotations (3)
Function System
Antitoxin of toxin-antitoxin stability system cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG6193H
(Mouseover regulator name to see its description)

VNG6193H is regulated by 37 influences and regulates 10 modules.
Regulators for VNG6193H (37)
Regulator Module Operator
VNG1510C
VNG6288C
17 combiner
VNG1786H 17 tf
VNG2112C 17 tf
VNG6143H 17 tf
VNG6389G 17 tf
VNG6438G 17 tf
VNG6438G
VNG6288C
17 combiner
VNG1179C 41 tf
VNG1237C 41 tf
VNG2112C 41 tf
VNG6143H 41 tf
VNG6389G 41 tf
VNG6438G 41 tf
VNG2112C 42 tf
VNG6143H 42 tf
VNG6389G 42 tf
VNG1510C 34 tf
VNG2112C 34 tf
VNG6143H 34 tf
VNG6438G 34 tf
VNG0247C 32 tf
VNG1237C 32 tf
VNG6143H 32 tf
VNG0462C 38 tf
VNG0869G 38 tf
VNG1886C 38 tf
VNG2112C 38 tf
VNG5163G 38 tf
VNG6143H 38 tf
VNG1548C 44 tf
VNG1616C
VNG0389C
44 combiner
VNG1886C 44 tf
VNG6143H 44 tf
VNG1510C 80 tf
VNG2112C 80 tf
VNG6389G 80 tf
VNG6438G 80 tf
Regulated by VNG6193H (10)
Module Residual Genes
86 0.33 23
106 0.31 15
134 0.24 2
149 0.25 2
171 0.24 2
186 0.39 7
219 0.29 3
227 0.47 28
290 0.20 2
298 0.36 28
Motif information (de novo identified motifs for modules)

There are 16 motifs predicted.

Motif Table (16)
Motif Id e-value Consensus Motif Logo
1013 1.70e-04 gtt.T.gcTagc.c.gtcTagTTa
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1014 8.40e-02 a.cGTcttcaTaatGataAca
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1041 9.60e+00 acTc.tgatTaAcA
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1042 2.00e+01 AcAcAcacgAgAcTg.gattA
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1045 0.00e+00 aaTAGaaAtCTTCtcTTcAcTGt
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1046 0.00e+00 AagacCaAtctgatgttaATTcaG
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1053 1.00e-06 TcaccaA..TaAagacGgatGa
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1054 1.20e-01 cTCTgAAtgAagAcA
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1059 3.50e+01 AatttcTctTgcGGAagta
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1060 1.20e+04 CcacGAcgAaCgCC
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1061 3.40e+00 acgatCttgtcgt.g
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1062 3.80e+04 ACTGACAGtaTATGT
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1065 3.40e+03 taagctCca.accCGGcAcat
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1066 8.30e+03 ccGCgAAcaaC
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1135 1.50e+03 aA.at..tTctgcGGaaa.t
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1136 1.50e+03 CgTCggTTcag
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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 VNG6193H

VNG6193H is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Antitoxin of toxin-antitoxin stability system cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for VNG6193H

VNG6193H has total of 106 gene neighbors in modules 17, 32, 34, 38, 41, 42, 44, 80
Gene neighbors (106)
Gene Common Name Description Module membership
VNG0030H hypothetical protein VNG0030H 32, 233, 239
VNG0031H hypothetical protein VNG0031H 32, 233, 239
VNG0032H hypothetical protein VNG0032H 32, 233, 239
VNG0055H hypothetical protein VNG0055H 37, 41, 183, 185
VNG0139H hypothetical protein VNG0139H 17, 18, 30, 196
VNG0148H hypothetical protein VNG0148H 41, 80, 171, 189, 196, 219, 224
VNG0181G lpl Lpl 32, 43
VNG0204H hypothetical protein VNG0204H 41
VNG0213H hypothetical protein VNG0213H 34, 35, 295
VNG0215C hypothetical protein VNG0215C 32, 92, 93, 94, 103, 104, 105
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
VNG0316C hypothetical protein VNG0316C 42, 68
VNG0430H hypothetical protein VNG0430H 42, 68, 151
VNG0462C hypothetical protein VNG0462C 42, 57, 68, 151, 162, 246
VNG0626G maoC2 molybdenum cofactor biosynthesis protein 80
VNG0761G dip3 competence-damage protein CinA-like 44, 151, 214
VNG0819C hypothetical protein VNG0819C 42
VNG0825C hypothetical protein VNG0825C 4, 5, 32, 43
VNG0836H hypothetical protein VNG0836H 42, 68
VNG0854C hypothetical protein VNG0854C 44
VNG0857Cm RNA methylase 44, 88
VNG0870G gatC hypothetical protein VNG0870G 42, 68
VNG0988H hypothetical protein VNG0988H 42, 68, 107, 203, 207, 210
VNG1064H hypothetical protein VNG1064H 17, 37, 96, 108
VNG1270H hypothetical protein VNG1270H 18, 30, 37, 42
VNG1525C hypothetical protein VNG1525C 41
VNG1534a birA biotin operon repressor and biotin-(acetyl-CoA carboxylase) ligase 41
VNG1650H hypothetical protein VNG1650H 4, 5, 30, 34, 35, 245, 295
VNG1732C hypothetical protein VNG1732C 80
VNG1779C hypothetical protein VNG1779C 44, 131, 230, 234
VNG1784C DNA primase 28, 42, 68, 83, 234
VNG1811G eye succinoglycan biosynthesis 42, 68, 179, 286
VNG1859G deoC hypothetical protein VNG1859G 42, 68
VNG1872C hypothetical protein VNG1872C 42, 68, 186
VNG1886C hypothetical protein VNG1886C 42, 68
VNG1891H hypothetical protein VNG1891H 14, 42, 68, 135
VNG1893G trp2 ABC transport protein 14, 42
VNG1894C hypothetical protein VNG1894C 14, 42
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
VNG1963H hypothetical protein VNG1963H 38
VNG1967G glpK hypothetical protein VNG1967G 44
VNG1969G gpdA2 glycerol-3-phosphate dehydrogenase chain A 44
VNG1971G gpdB anaerobic glycerol-3-phosphate dehydrogenase subunit B 20, 44
VNG1986C hypothetical protein VNG1986C 17, 26, 30, 31, 108
VNG2024H hypothetical protein VNG2024H 38
VNG2034H hypothetical protein VNG2034H 41
VNG2174H hypothetical protein VNG2174H 34, 38, 297
VNG2185H hypothetical protein VNG2185H 41
VNG2298H hypothetical protein VNG2298H 42, 68, 152
VNG2317G cbiO1 cobalt transport ATP-binding protein 38, 48, 178
VNG2414H hypothetical protein VNG2414H 18, 38, 64
VNG2444C hypothetical protein VNG2444C 17, 28, 31, 38, 173
VNG2454C hypothetical protein VNG2454C 32
VNG2632G yusZ2 oxidoreductase 34, 41, 143
VNG2669G cyo cytochrome oxidase subunit I-like protein 44, 179
VNG5150H None 38, 42
VNG5168H None 38
VNG5175H None 42, 68, 234
VNG6142C hypothetical protein VNG6142C 42, 68, 295
VNG6144G trsE transfer complex protein 4, 5, 42, 68, 295
VNG6148H hypothetical protein VNG6148H 42, 68
VNG6150G orc1 orc / cell division control protein 6 4, 13, 38, 142, 189
VNG6158H hypothetical protein VNG6158H 42, 68
VNG6160H hypothetical protein VNG6160H 38
VNG6168H hypothetical protein VNG6168H 38, 42
VNG6187G orc3 orc / cell division control protein 6 42, 68
VNG6191H hypothetical protein VNG6191H 17, 30, 34, 38, 41, 44, 80, 91
VNG6193H hypothetical protein VNG6193H 17, 32, 34, 38, 41, 42, 44, 80
VNG6194H hypothetical protein VNG6194H 34
VNG6196G phoT2 sodium-dependent phosphate transporter 30, 36, 41, 80, 87, 89
VNG6197H hypothetical protein VNG6197H 38, 108
VNG6203H hypothetical protein VNG6203H 42
VNG6229G gvpL2 GvpL protein, cluster B 38, 141, 188
VNG6232G gvpJ2 GvpJ protein, cluster B 4, 5, 8, 28, 31, 42, 141, 148, 182, 188
VNG6235G gvpH2 GvpH protein, cluster B 31, 42, 141, 188
VNG6242G gvpC2 GvpC protein, cluster B 42, 185
VNG6291H hypothetical protein VNG6291H 38
VNG6292C hypothetical protein VNG6292C 17, 18, 30, 89
VNG6293C hypothetical protein VNG6293C 17
VNG6322H hypothetical protein VNG6322H 17, 168, 178
VNG6325H hypothetical protein VNG6325H 80
VNG6327H hypothetical protein VNG6327H 41
VNG6344H hypothetical protein VNG6344H 17, 41
VNG6349C hypothetical protein VNG6349C 17
VNG6359H hypothetical protein VNG6359H 17, 157, 271
VNG6389G tfbE transcription initiation factor IIB 34
VNG6390H hypothetical protein VNG6390H 4, 26, 30, 34, 35, 245, 295
VNG6396H hypothetical protein VNG6396H 38
VNG6397H hypothetical protein VNG6397H 38
VNG6400H hypothetical protein VNG6400H 18, 30, 80, 133, 245, 290
VNG6401H hypothetical protein VNG6401H 80, 133, 237, 248
VNG6402H hypothetical protein VNG6402H 80
VNG6416H hypothetical protein VNG6416H 13, 15, 21, 41, 60, 281
VNG6418H hypothetical protein VNG6418H 13, 18, 21, 41, 60, 281
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
VNG7011 repH plasmid replication protein RepH 17, 18, 30, 107, 122, 224, 287
VNG7013 hypothetical protein VNG7013 80
VNG7073 hypothetical protein VNG7073 34, 35, 245, 295
VNG7109 hypothetical protein VNG7109 4, 18, 38, 91
VNG7110 hypothetical protein VNG7110 18, 38, 91, 147
VNG7138 hypothetical protein VNG7138 34, 35, 245, 295
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 VNG6193H
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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