Table 2 Computational tools and resources for the analyses of noncoding risk locia

From: Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies

Feature

Description

Significance

Experimental approach

Bioinformatic tools and online resources

Open chromatin

Nucleosome-depleted chromatin

DNA sequences harboring regulatory signals

DNase-seq, FAIRE sequencing

ENCODE,96 REMC,97

RegulomeDB,98 HaploReg,99 FunciSNP101

TF-binding prediction

Short DNA consensus recognition sequence characteristic of a particular DNA-binding protein

Computationally predicted TF recognition site

Position weight matrices

TRANSFAC,154 JASPAR,155 MAPPER2,156 GWAS3D,157 DeepSEA158

DNA–protein interaction

Short DNA sequence associated with a DNA-binding protein after precipitation with a specific antibody

Physical protein-nucleic-acid binding

ChIP-seq, DNase footprinting

ENCODE,96 NRCistrome,159

RegulomeDB,98 HaploReg,99 GWAVA100

DNA methylation

Methylation of cytosine residues in CpG dinucleotides

Regulation of gene expression

Methylation array, bisulfite sequencing, MeDIP-seq, MRE-seq

ENCODE,96 REMC,97

MethDB,160, 161 EpiGraph,162 BrainCloudMethyl,163 Fetal brain meQTLs107

DNase I hypersensitive sites

Sensitive to cleavage by the DNase I enzyme

DNA sequences harboring regulatory signals

DNase-seq

ENCODE,96 REMC,97

PsychENCODE,113 DeepSEA158

Histone modifications

Specific posttranslational modifications of particular histone protein residues are associated with various regulatory activities

H3K4me1: promoters and enhancers

H3K4me3: promoters

H3K27ac: active regulatory region

H3K9ac: promoters

H3K9me1: active chromatin

ChIP-seq

ENCODE,96 REMC,97

PsychENCODE,113

NRCistrome,159

RegulomeDB,98 HaploReg,99 ChromHMM,164

GWAS3D,157 ChroMoS,165 SEA,166 DeepSEA158

Chromatin interactions

Long-range physical interactions between distal genomic regions

Contact between regulatory motifs, such as tissue-specific enhancers and promoters

3C, 4C, 5C, Hi-C, ChIA-PET

GWAS3D,157 Hi-C Browser,167 CCSI168

MicroRNA-binding prediction

Short DNA consensus recognition sequence characteristic of a particular microRNA

Computationally predicted microRNA recognition site

Position weight matrices

miRanda,169 Target Scan,170 MicroSNiPer171

  1. Abbreviations: 3C, chromosome conformation capture; 4C, circular 3C; 5C, carbon-copy 3C; CCSI, Chromatin Chromatin Space Interaction; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; ChIP-Seq, chromatin immunoprecipitation followed by next-generation sequencing; DNase-seq, DNase I hypersensitive site sequencing; FAIRE, formaldehyde-assisted isolation of regulatory elements; MeDIP-seq, methylated DNA immunoprecipitation sequencing; MRE-seq, methylation-sensitive restriction enzyme sequencing; NRCistrome, Nuclear Receptor Cistrome; REMC, NIH Roadmap Epigenomics Project; RNA-PET, RNA paired-end tag sequencing; SEA, super-enhancer archive; TF, transcription factor.
  2. Websites: ENCODE https://www.encodeproject.org/.
  3. REMC http://www.roadmapepigenomics.org/.
  4. RegulomeDB http://www.regulomedb.org.
  5. HaploReg http://www.broadinstitute.org/mammals/haploreg.
  6. FunciSNP http://bioconductor.org/packages/2.12/bioc/html/FunciSNP.html.
  7. TRANSFAC http://www.gene-regulation.com/index2.
  8. MAPPER2 http://genome.ufl.edu/mapperdb.
  9. GWAS3D http://jjwanglab.org/gwas3d/.
  10. DeepSEA http://deepsea.princeton.edu/job/analysis/create/.
  11. NRCistrome http://www.cistrome.org/Cistrome/Cistrome_Project.html.
  12. GWAVA http://www.sanger.ac.uk/sanger/StatGen_Gwava.
  13. MethDB http://www.methdb.de.
  14. EpiGRAPH http://epigraph.mpi-inf.mpg.de/WebGRAPH/.
  15. BrainCloudMethyl http://braincloud.jhmi.edu/Methylation64/BrainCloudMethyl64bit.htm.
  16. Fetal brain meQTLs http://epigenetics.essex.ac.uk/mQTL/.
  17. PsychENCODE http://psychencode.org/.
  18. ChromHMM http://compbio.mit.edu/ChromHMM/.
  19. ChroMoS http://epicenter.immunbio.mpg.de/services/chromos.
  20. SEA http://www.bio-bigdata.com/SEA/.
  21. Hi-C Browser http://hic.umassmed.edu/welcome/welcome.php.
  22. CCSI http://songyanglab.sysu.edu.cn/ccsi/search.php.
  23. miRanda http://www.microrna.org/microrna/home.do.
  24. Target Scan http://www.targetscan.org/vert_71/.
  25. MicroSNiPer http://epicenter.ie-freiburg.mpg.de/services/microsniper/.
  26. aNonexhaustive list of examples.
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