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Regul@tionSpotter

Documentation

Documentation
Input Output Interaction Plot Contact
Examples
Examples & Tutorial

Analysing a single variant

Input

Single Variant

For single queries in RegulationSpotter you can use the single query interface. Here, you can put in single variants as shown in our single query tutorial. Simply fill in the chromosome and location of the variant along with the reference and alternative allele. Please note the instructions for the Indel input.

Output: detailed

Clicking the submit button of a single query or on one of the variants of a vcf file leads you to more detailed insight into your results. For intragenic alterations and known disease causing variants, you will be redirected to our conventional MutationTaster output. More information can be found in the MutationTaster documentation.

Screenshot of a single variant result file

Screenshot of a single variant result file. To see all details of the specific result see click here.



Results

Likely effect of an alteration. RegulationSpotter treats alterations differently depending on whether they are located within a gene or not. For intragenic alterations, it relies on MutationTaster, which classifies an alteration as one of four possible types:

disease causing (ClinVar): known disease mutation listed in ClinVar.
disease causing: predicted by MutationTaster as disease causing.
polymorphism: predicted by MutationTaster as harmless.
polymorphism automatic: known to be harmless from databases.

For more details about the classification process, please refer to our MutationTaster documentation.

Extragenic alterations are assessed by RegulationSpotter directly. The program compiles and combines all the regulatory data and comes up with an estimate of how likely it is for a variant to be located in a regulatory region. The three possible outcomes are:

likely functional: Regulatory information is available for the variant's location in several data sources. Thus, RegulationSpotter considers the likelihood for a regulatory function to be quite high.
possibly functional: Regulatory information is available for the variant's location in at least one data source.
polymorphism: No regulatory information is available. Thus, RegulationSpotter assumes that the variant is not located in a regulatory region.

Alteration (phys. location)

The alteration on "physical" i.e. chromosomal level (e.g. chr7:91623937_91623938insGGCAAT).

Alteration type

Is either a base exchange, a combination of insertion and deletion, an insertion or a deletion.

Alteration region

Extragenic by definition.

Known variant

Any known polymorphism(s) or known disease variant that have been found at the position in question. Our database contains all single nucleotide polymorphisms (SNPs) from the NCBI SNP database (dbSNP). Moreover, we have stored all HapMap genotype frequencies as well as variants from the 1000 Genomes Project [3] (TGP). If an alteration is located at the same position as a known dbSNP, RegulationSpotter provides the SNP ID (or rs ID) and a link together with the HapMap genotype frequencies, if available. If every of the three possible genotypes is observed in at least one HapMap population, the alteration is automatically regarded as a polymorphism and predicted as polymorphism automatic. Please note that there may be differences between your alteration and the alleles in dbSNP.
For TGP, RegulationSpotter provides information in either of the following formats: If an alteration was found more than 4 times homozygously in TGP, it is automatically regarded as polymorphism. We also display known disease variants from dbSNP ClinVar. If a variant is marked as probable-pathogenic or pathogenic in ClinVar, it is automatically predicted to be disease-causing, i.e. disease causing automatic (the naive Bayes classifier is run nevertheless and the p value for the prediction is shown). Moreover, we have integrated the public version of the Human Gene Mutation Database (HGMD) [5]. The data includes the positions of the disease mutations and their HGMD ID. The disease alleles are not included so we cannot use HGMD for automatic predictions. Whenever an HGMD public disease mutation is found at the same position as a variant, this will be written in the summary. We also place a direct hyperlink to the mutation in HGMD into the 'dbSNP / TGP / HGMD(public) / ClinVar' field, so you can check whether the HGMD mutation has the same allele as your variant (and whether the disease matches). Please note that you must be logged in at the HGMD site to make the hyperlink work - access to the public version is free but requires registration.

ENSEMBL multicell regulatory features

Indicates whether the alteration is located within an ENSEMBL multicell regulatory feature.

ENSEMBL detailed regulatory features

Lists all ENSEMBL features detected at the variant location in detail as can be seen below.

Histone_modifications

H2AK5acHistone 2A Lysine 5 Acetylation
H2AZHistone 2A variant Z
H2BK120acHistone 2B Lysine 120 Acetylation
H2BK12acHistone 2B Lysine 12 Acetylation
H2BK15acHistone 2B Lysine 15 Acetylation
H2BK20acHistone 2B Lysine 20 Acetylation
H2BK5acHistone 2B Lysine 5 Acetylation
H3K14acHistone 3 Lysine 14 Acetylation
H3K18acHistone 3 Lysine 18 Acetylation
H3K23acHistone 3 Lysine 23 Acetylation
H3K23me2Histone 3 Lysine 23 di-methylation
H3K27acHistone 3 Lysine 27 Acetylation
H3K27me3Histone 3 Lysine 27 Tri-Methylation
H3K36me3Histone 3 Lysine 36 Tri-Methylation
H3K4acHistone 3 Lysine 4 Acetylation
H3K4me1Histone 3 Lysine 4 Mono-Methylation
H3K4me2Histone 3 Lysine 4 Di-Methylation
H3K4me3Histone 3 Lysine 4 Tri-Methylation
H3K56acHistone 3 Lysine 56 Acetylation
H3K79me1Histone 3 Lysine 79 mono-methylation
H3K79me2Histone 3 Lysine 79 di-methylation
H3K9acHistone 3 Lysine 9 Acetylation
H3K9me1Histone 3 Lysine 9 mono-methylation
H3K9me3Histone 3 Lysine 9 Tri-Methylation
H4K20me1Histone 4 Lysine 20 mono-methylation
H4K5acHistone 4 Lysine 5 Acetylation
H4K8acHistone 4 Lysine 8 Acetylation
H4K91acHistone 4 Lysine 91 Acetylation

Open chromatin regions

DNase1DNase1 Hypersensitive Site

Polymerase

PolIIRNA Polymerase II
PolIIIRNA Polymerase III Binding

TF binding sites

Ap2alphaAp2alpha Transcription Factor Binding
Ap2gammaAp2gamma Transcription Factor Binding
ATF3ATF3 Transcription Factor Binding
BAF155BAF155 Transcription Factor Binding
BAF170BAF170 Transcription Factor Binding
BATFBATF Transcription Factor Binding
BCL11ABCL11A Transcription Factor Binding
BCL3BCL3 Transcription Factor Binding
BCLAF1BCLAF1 Transcription Factor Binding
BHLHE40BHLHE40 Transcription Factor Binding
Brg1Brg1 Transcription Factor Binding
CfosCfos TF binding
CjunCjun TF binding
CmycCmyc TF binding
CTCFCCCTC-binding factor
CTCFLCTCFL Transcription Factor Binding
E2F1E2F1 Transcription Factor Binding
E2F4E2F4 Transcription Factor Binding
E2F6E2F6 Transcription Factor Binding
EBF1EBF1 Transcription Factor Binding
Egr1Egr1 Transcription Factor Binding
ELF1ELF1 Transcription Factor Binding
ETS1ETS1 Transcription Factor Binding
FOSL1FOSL1 Transcription Factor Binding
FOSL2FOSL2 Transcription Factor Binding
FOXA1FOXA1 Transcription Factor Binding
FOXA2FOXA2 Transcription Factor Binding
GabpGabp TF binding
Gata1Gata1 TF binding
Gata2Gata2 Transcription Factor Binding
GTF2BGTF2B Transcription Factor Binding
HDAC2HDAC2 Transcription Factor Binding
HDAC8HDAC8 Transcription Factor Binding
HEY1HEY1 Transcription Factor Binding
HNF4AHNF4A Transcription Factor Binding
HNF4GHNF4G Transcription Factor Binding
Ini1Ini1 Transcription Factor Binding
IRF4IRF4 Transcription Factor Binding
JunbJunb Transcription Factor Binding
JundJund TF binding
MaxMax TF binding
MEF2AMEF2A Transcription Factor Binding
MEF2CMEF2C Transcription Factor Binding
NanogNanog Transcription Factor Binding
Nfe2Nfe2 TF binding
NFKBNFKB Transcription Factor Binding
NR4A1NR4A1 Transcription Factor Binding
Nrf1Nrf1 Transcription Factor Binding
NrsfNrsf TF binding
p300p300 Transcription Factor Binding
Pax5Pax5 Transcription Factor Binding
Pbx3Pbx3 Transcription Factor Binding
POU2F2POU2F2 Transcription Factor Binding
POU5F1POU5F1 Transcription Factor Binding
PU1PU1 Transcription Factor Binding
Rad21Rad21 Transcription Factor Binding
RXRARXRA Transcription Factor Binding
SETDB1SETDB1 Transcription Factor Binding
Sin3Ak20Sin3Ak20 Transcription Factor Binding
SIX5SIX5 Transcription Factor Binding
SP1SP1 Transcription Factor Binding
SP2SP2 Transcription Factor Binding
SrfSrf TF binding
TAF1TAF1 Transcription Factor Binding
TAF7TAF7 Transcription Factor Binding
Tcf12Tcf12 Transcription Factor Binding
THAP1THAP1 Transcription Factor Binding
Tr4Tr4 Transcription Factor Binding
USF1USF1 Transcription Factor Binding
XRCC4XRCC4 Transcription Factor Binding
Yy1Yy1 Transcription Factor Binding
ZBTB33ZBTB33 Transcription Factor Binding
ZBTB7AZBTB7A Transcription Factor Binding
ZEB1ZEB1 Transcription Factor Binding
Znf263Znf263 TF binding
ZNF274ZNF274 Transcription Factor Binding

Other regulatory features

Obsolete...will be changed.

Regulatory features from VISTA and FANTOM5

Regulatory data from Ensembl Regulatory build, b37, published in [2] (FANTOM5) and [4] (VISTA).

TarBase miRNA binding sites

MicroRNA binding sites which are affected by the alteration as annotated in DIANA TarBase [2;5].
A link to Diana TarBase with more information to the respective microRNA is provided.

Interactions with distant genomic regions

Shows all interactions of the variant location with other regulatory regions such as promoters or enhancers. Thus, even though the variant is not located within a gene, these data indicate if it falls into a region associated to a gene. In this case the variant is more likely to be functional and the interaction data informs you about the genes and the specific elements that might be affected by this, as well as the cell types for which this interaction is true and the associated transcripts of that location. If RegulationSpotter finds any interactions it also creates a graphic output of the interaction:

Interaction plot

Screenshot of a single variant result file

Screenshot of an interaction plot. To see all details of the specific result see
click here and select the interaction plot from the results output.
The thin red line symbolizes the location of the variant. Interaction elements are depicted as blue rectangles. You can find genes in the region as red rectangles and pseudogenes marked with a little green box. Moreover, You will find a link to explore the variant in Ensembl. Below the plot you can find the evidence found for this interactions as described in Interactions with distant genomic regions.


PhyloP/PhastCons

Indicates the conservation of the alteration site. Data from phyloP [6] and PhastCons [7].
PhastCons and phyloP are both methods to determine the grade of conservation of a given nucleotide. RegulationSpotter uses values which are precomputed and offered by UCSC (please follow the links to phyloP and PhastCons).
phastCons values vary between 0 and 1 and reflect the probability that each nucleotide belongs to a conserved element, based on the multiple alignment of genome sequences of 46 different species (the closer the value is to 1, the more probably the nucleotide is conserved). It considers not just each individual alignment column, but also its flanking columns.
In contrast, phyloP (values between -14 and +6) separately measures conservation at individual columns, ignoring the effects of their neighbors. Moreover, phyloP can not only measure conservation (slower evolution than expected under neutral drift) but also acceleration (faster evolution than expected). Sites predicted to be conserved are assigned positive scores, while sites predicted to be fast-evolving are assigned negative scores.
For more information about phyloP and phastCons, please see the cited papers.

Chromosome

The chromosome the alteration is located on.

Strand

Is either 1 for forward strand or -1 for reverse strand

Chromosomal position

Gives the last wild-type base before alteration and first wild-type base after alteration in chromosomal sequence context (position relative to start of chromosomal reference sequence) e.g. 154,372,337 / 154,372,339, the altered base is at position 154,372,338.

Original chrDNA sequence snippet

Original DNA sequence with the original nucleotide marked in blue.

Altered chrDNA sequence snippet

Altered DNA sequence with the original nucleotide marked in blue.

Contact

In case you discover bugs, have suggestions or questions, please write an e-mail to
Jana Marie Schwarz (jana-marie.schwarz AT charite.de) or to
Dominik Seelow
(dominik.seelow AT charite.de).
We also appreciate hearing about your general experiences using RegulationSpotter.

References

[1] Rao SS, Huntley MH, Durand NC, Stamenova EK et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 2014. PMID: 25497547

[2] Zerbino DR, Wilder SP, Johnson N, Huettemann T, Flicek PR. The Ensembl Regulatory Build. Genome Biology 2015. PMID: 25887522

[3] 1000 Genomes Project Consortium: An integrated map of genetic variation from 1,092 human genomes. Nature 2012 Nov 1. PMID: 23128226

[4] Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA Enhancer Browser - a database of tissue-specific human enhancers. Nucleic Acids Res. 2007. PMID: 17130149

[5] Vlachos IS, Paraskevopoulou MD, Karagkouni D et al. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res. 2014. PMID: 25416803

[6] Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates on mammalian phylogenies. Genome Res. 2009. PMID: 19858363

[7] Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005. PMID: 16024819