Organism : Halobacterium salinarum NRC-1 | Module List :
VNG0258H

hypothetical protein VNG0258H

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulators cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for VNG0258H
(Mouseover regulator name to see its description)

VNG0258H is regulated by 41 influences and regulates 21 modules.
Regulators for VNG0258H (41)
Regulator Module Operator
VNG0040C
VNG0293H
3 combiner
VNG0703H
VNG2641H
3 combiner
VNG1029C 3 tf
VNG1029C
VNG2641H
3 combiner
VNG0194H 49 tf
VNG0254G 49 tf
VNG0293H
VNG0703H
49 combiner
VNG0734G
VNG2641H
49 combiner
VNG1029C 49 tf
VNG1123G 49 tf
VNG1464G
VNG1029C
49 combiner
VNG1496G
VNG0320H
49 combiner
VNG2163H 49 tf
VNG2243G 49 tf
VNG0040C
VNG0293H
79 combiner
VNG0293H
VNG0703H
79 combiner
VNG0703H
VNG2641H
79 combiner
VNG1029C
VNG2641H
79 combiner
VNG0040C
VNG0293H
100 combiner
VNG0194H 100 tf
VNG0254G 100 tf
VNG1836G
VNG1899G
100 combiner
VNG0040C
VNG0293H
109 combiner
VNG0254G 109 tf
VNG0734G
VNG0293H
109 combiner
VNG0734G
VNG0424C
109 combiner
VNG2243G
VNG0293H
109 combiner
VNG0101G 150 tf
VNG0315G 150 tf
VNG1123G 150 tf
VNG1836G
VNG0374G
150 combiner
VNG2661G
VNG1483C
150 combiner
VNG0040C
VNG0293H
12 combiner
VNG0293H
VNG0703H
12 combiner
VNG1029C
VNG2641H
12 combiner
VNG1496G
VNG0320H
12 combiner
VNG0040C
VNG0293H
16 combiner
VNG0101G
VNG0320H
16 combiner
VNG0101G
VNG2163H
16 combiner
VNG1836G 16 tf
VNG2661G
VNG1029C
16 combiner
Regulated by VNG0258H (21)
Module Residual Genes
2 0.35 31
7 0.37 29
19 0.34 16
29 0.36 26
39 0.35 33
50 0.36 31
55 0.35 14
71 0.36 23
75 0.49 7
78 0.32 20
81 0.45 7
88 0.37 20
98 0.59 12
113 0.36 32
123 0.31 18
128 0.39 6
156 0.41 4
187 0.40 23
191 0.56 30
199 0.47 7
283 0.56 30
Motif information (de novo identified motifs for modules)

There are 16 motifs predicted.

Motif Table (16)
Motif Id e-value Consensus Motif Logo
985 2.00e-06 at.tttgTtttttgat.gccgtt
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986 1.40e+01 aAa.gttTtA.T
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1003 8.00e-06 g.AAatctttaAgT
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1004 1.00e-01 agaaAt.gg.TgT.cgtAT
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1011 2.80e-04 caatttataggtTttcAcctt
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1012 1.20e+01 AaaagGGtTttcgTATcgccGT
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1075 7.90e-01 aGAaAAttgtTga
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1076 7.90e+00 gaAtcgaacggaAagcaTtaAgT
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1133 2.60e-04 Aaat.tgtttcatGtgAgaaaa
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1134 3.30e+01 GCGatacgaaAaCc.tT.ttC
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1175 4.50e+01 A.AagTtttTA
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1176 3.40e+03 ATTTAA
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1191 8.10e-01 CaGgaaAgaaatGTtTaAaTG
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1192 1.10e+01 GgcGCgcCCCACACCTcCaaC
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1265 8.60e-01 tTcaAC.ctttt.a
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1266 1.50e+03 AGTGAA
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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 VNG0258H

VNG0258H is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for VNG0258H

VNG0258H has total of 81 gene neighbors in modules 3, 12, 16, 49, 79, 100, 109, 150
Gene neighbors (81)
Gene Common Name Description Module membership
VNG0042G ntp transposase 150, 187
VNG0161G gdhB glutamate dehydrogenase 3, 123
VNG0162G alkK AlkK 3, 12, 49, 113, 123
VNG0192G ftsZ2 cell division protein FtsZ 2, 3, 7, 12, 16, 49, 50, 71, 78, 79, 123
VNG0194H hypothetical protein VNG0194H 3, 7, 12, 16, 50, 79, 123
VNG0207H hypothetical protein VNG0207H 2, 3, 7, 12, 16, 49, 67, 71, 78, 79, 113, 123
VNG0208H hypothetical protein VNG0208H 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123
VNG0209H hypothetical protein VNG0209H 2, 3, 7, 12, 16, 24, 29, 49, 67, 71, 78, 79, 113, 123
VNG0234C hypothetical protein VNG0234C 2, 16
VNG0254G tfbG transcription initiation factor IIB 3, 12, 25, 50, 55, 113
VNG0258H hypothetical protein VNG0258H 3, 12, 16, 49, 79, 100, 109, 150
VNG0259G ipp inorganic pyrophosphatase 7, 12, 16, 79, 109
VNG0261H hypothetical protein VNG0261H 7, 12, 16, 25, 49, 50, 55, 79, 109, 113
VNG0262C hypothetical protein VNG0262C 12, 25, 49, 50, 55, 79, 109, 113
VNG0264H hypothetical protein VNG0264H 55, 109
VNG0282H hypothetical protein VNG0282H 109
VNG0524G yurY ABC transporter ATP-binding protein 2, 3, 7, 12, 16, 71, 113, 225
VNG0525C hypothetical protein VNG0525C 7, 12, 71, 78, 113, 225
VNG0527C hypothetical protein VNG0527C 2, 3, 7, 12, 16, 71, 78, 79, 113, 123, 225
VNG0579H hypothetical protein VNG0579H 49, 79, 123, 187
VNG0582C hypothetical protein VNG0582C 16, 283
VNG0584H hypothetical protein VNG0584H 2, 16, 24
VNG0585H hypothetical protein VNG0585H 2, 16, 24
VNG0586C hypothetical protein VNG0586C 79, 187
VNG0620G edp proteinase IV-like protein 2, 16
VNG0635G nolB NADH dehydrogenase/oxidoreductase-like protein 2, 16, 19, 24, 29, 199
VNG0637G ndhG5 NADH dehydrogenase/oxidoreductase 2, 16, 19, 24, 29
VNG0640G nolD NADH dehydrogenase/oxidoreductase-like protein 2, 3, 16, 19, 24, 29, 45, 123
VNG0771G aldY2 AldY2 16, 123
VNG0801C hypothetical protein VNG0801C 12, 49, 71, 79, 113, 187
VNG0849C hypothetical protein VNG0849C 100, 283
VNG0880G psmA proteasome subunit alpha 12, 49, 71, 79, 109
VNG0906H hypothetical protein VNG0906H 71, 79
VNG0940Gm ACS3 Acetyl-CoA synthetase 7, 19, 24, 25, 29, 49
VNG0955G fapE flagella-like protein E 7, 16, 25, 50, 100, 291
VNG0960G flaB1 flagellin B1 2, 3, 7, 12, 16, 49, 78, 79, 100, 113, 123
VNG0961G flaB2 flagellin B2 2, 3, 7, 12, 16, 49, 78, 79, 100, 113, 123, 291
VNG0962G flaB3 flagellin B3 2, 3, 7, 12, 16, 49, 78, 100, 113, 123
VNG0963G cpcE phycocyanin alpha phycocyanobilin lyase-like protein 12, 79
VNG0964C hypothetical protein VNG0964C 12, 24, 49, 100, 109
VNG0999H hypothetical protein VNG0999H 79, 187
VNG1002H hypothetical protein VNG1002H 49, 242
VNG1093C hypothetical protein VNG1093C 71, 79, 187
VNG1103G rpl12p 50S ribosomal protein L12P 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1104G rplP0 acidic ribosomal protein P0 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1105G rpl1P 50S ribosomal protein L1P 1, 10, 39, 66, 82, 99, 137, 150, 161, 165, 180
VNG1108G rpl11p 50S ribosomal protein L11P 1, 66, 82, 137, 150, 161, 165, 180
VNG1111G drg GTP-binding protein DRG 1, 82, 137, 150, 161
VNG1114G glo1 glyoxalase 1, 82, 137, 150, 161, 165, 180
VNG1125G korB KorB 7, 12, 24, 29
VNG1128G korA KorA 3, 7, 12, 24, 29, 49, 71, 78, 113
VNG1149Cm metallo-beta-lactamase superfamily hydrolase 2, 16, 23, 33
VNG1189H hypothetical protein VNG1189H 79, 187
VNG1261H hypothetical protein VNG1261H 49, 113
VNG1306G sdhA hypothetical protein VNG1306G 2, 3, 12, 16, 78, 79, 90, 100
VNG1332G sod2 superoxide dismutase 100
VNG1412H hypothetical protein VNG1412H 3, 12, 49, 71, 79, 113
VNG1688C hypothetical protein VNG1688C 150
VNG1809H hypothetical protein VNG1809H 150
VNG1836G cspD2 cold shock protein 3, 12, 49, 71, 79
VNG1907H hypothetical protein VNG1907H 150
VNG2006C hypothetical protein VNG2006C 79, 113, 170, 187
VNG2008H hypothetical protein VNG2008H 9, 49, 79, 113, 170, 187
VNG2044H hypothetical protein VNG2044H 79, 187
VNG2081H hypothetical protein VNG2081H 49, 50, 123, 175, 187
VNG2122G ilvE2 branched-chain amino acid aminotransferase 7, 19, 29, 49, 71, 75, 78
VNG2135G atpD V-type ATP synthase subunit D 2, 16
VNG2146H hypothetical protein VNG2146H 2, 16, 19, 24, 45, 67, 124, 227
VNG2226G cctA thermosome subunit alpha 3, 7, 12, 29, 49, 50, 52, 78, 113
VNG2251G achY S-adenosyl-L-homocysteine hydrolase 24, 29, 49, 71, 79, 113
VNG2293G fer2 ferredoxin 3, 110, 113
VNG2337C hypothetical protein VNG2337C 16, 29, 49, 113
VNG2443G dpsA starvation induced DNA-binding protein 3, 12, 49, 71, 79, 113, 123, 187
VNG2543C hypothetical protein VNG2543C 3, 12, 49, 71, 78, 113, 156
VNG2648G rps10p 30S ribosomal protein S10P 2, 3, 16, 23, 24, 29, 40, 110
VNG2649G eef1a elongation factor 1-alpha 2, 3, 16, 24, 29, 40, 79, 110
VNG2666G rpoB'' DNA-directed RNA polymerase subunit beta'' 2, 16, 40, 98, 110
VNG6201G hsp5 heat shock protease protein 3, 49, 71, 79, 98, 100, 113, 187, 240
VNG6313G nhaC3 Na+/H+ antiporter 2, 3, 12, 16, 50, 113
VNG7002 hypothetical protein VNG7002 150
VNG7101 hypothetical protein VNG7101 49, 71, 113
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 VNG0258H
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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