dbMTS version 1.0

Release: 9-Jul-19

Files:

dbMTS1.0.chr<#>.gz - gzipped dbMTS variant database files by chromosomes

dbMTS1.0_gene.gz - gzipped dbMTS gene by miRNA target count matrix table

dbMTS1.0.readme.txt - this file

Description:

dbMTS collects all potential SNVs microRNA target seed regions in human 3'UTRs and provides their functional predic and annotations to facilitate the steps of filtering and prioritizing SNVs from a huge list of all SNVs discovered in a whole exome sequencing (WES) study. The core functional annotations in the database are the targeting efficacy scores for "the reference and mutant loci based on three microRNA target prediction algorithms, TargetScan v7.0, RNAhybrid, and miRanda. " "Based on their predictions, we further classify the effect of each SNV into three categories, substitution, target loss and " target gain. The maximum difference between the reference score and variant-induced score was calculated to estimate how the microRNA targeting efficacy was changed after introducing the variant. Additional functional annotations of the SNVs "were also collected in dbMTS including variant consequences by SnpEff, VEP and ANNOVAR, dbSNP variant IDs, GWAS Catalog " "entries, allele frequencies from various populations, clinical consequences from ClinVar, expression quantitative trait " "loci (eQTLs) from GTEx, mappability scores etc."

Contact:

Xiaoming Liu, Ph.D."
Associate Professor,"
USF Genomics,"
College of Public Health,"
University of South Florida
Email: xmliu.uth{at}gmail.com

Cells in dbMTS1.0_gene.gz:

Each cell has three values separated by |, which correspond to the number of targets for the pair of transcript and" miRNA predicted by miRanda, TargetScan and RNAhybrid, respectively. "

Columns of dbMTS1.0.chr<#>.gz:

1 chr: chromosome number
2 pos: position (hg38)
3 ref: reference allele
4 alt: alternative allele
5 chr_hg19: chromosome number based on human reference sequence version hg19 (GRCh19)
6 pos_hg19: position based on human reference sequence version hg19 (GRCh19)
7 ref_hg19: reference allele based on human reference sequence version hg19 (GRCh19)
8 alt_hg19: alternative allele based on human reference sequence version hg19 (GRCh19) this column shall be identical to column ""alt"" if ref_hg19=ref_hg38 is Y(es) or be ""."" if ref_hg19=ref_hg38 is N(o) "
9 ref_hg19=ref_hg38: whether the reference allele based on hg19 identical to that based on hg38
10 VEP_ensembl_Consequence: VEP consequence with Ensembl as gene model. Multiple consequences are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
11 VEP_ensembl_Transcript_ID: Ensembl transcript IDs corresponding to consequences. Multiple IDs are separated by ""|"""
12 VEP_ensembl_Gene_Name: Ensembl gene names corresponding to transcripts. Multiple gene names are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
13 VEP_ensembl_Gene_ID: Ensembl gene IDs corresponding to transcripts. Multiple IDs are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
14 VEP_ensembl_Protein_ID: Ensembl protein IDs corresponding to transcripts. Multiple IDs are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
15 VEP_ensembl_CCDS: CCDS IDs corresponding to transcripts. Multiple IDs are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
16 VEP_ensembl_SWISSPROT: SWISSPROT IDs corresponding to transcripts. Multiple IDs are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
17 VEP_ensembl_Codon_Change_or_Distance: codon change or distance as to a transcript. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
18 VEP_ensembl_Amino_Acid_Change: amino acid change as to a transcript. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
19 VEP_ensembl_HGVSc: variant in format of HGVSc. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
20 VEP_ensembl_HGVSp: variant in format of HGVSp. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
21 VEP_ensembl_cDNA_position: cDNA position as to a transcript. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
22 VEP_ensembl_CDS_position: CDS position as to a transcript. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
23 VEP_ensembl_Protein_position: protein position as to a transcript. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
24 VEP_ensembl_Exon_or_Intron_Rank: exon (intron) rank as to a transcript. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
25 VEP_ensembl_STRAND: strand of CDS as to a transcript. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
26 VEP_ensembl_CANONICAL: whether a transcript is canonical. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
27 VEP_ensembl_LoF: LOF by LOFTEE. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
28 VEP_ensembl_LoF_filter: LOF filter by LOFTEE. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
29 VEP_ensembl_LoF_flags: LOF flags by LOFTEE. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
30 VEP_ensembl_LoF_info: LOF information by LOFTEE. Multiple annotations are separated by ""|"" The order corresponds to VEP_ensembl_Transcript_ID"
31 VEP_ensembl_summary: VEP consequence summary with Ensembl as gene model. Format
32 rs_dbSNP150: rs number from dbSNP150
33 GWAS_catalog_rs: rs number according to GWAS catalog
34 GWAS_catalog_trait: associated trait according to GWAS catalog
35 GWAS_catalog_pubmedid: pubmedid of the paper describing the association
36 GRASP_rs: rs number by GRASP
37 GRASP_PMID: PMID number by GRASP
38 GRASP_p-value: p-value of the association test based on the SNP
39 GRASP_phenotype: phenotype the SNP associated with
40 GRASP_ancestry: population ancestry of the samples on which the association test was based
41 GRASP_platform: SNP platform on which the association test was based
42 clinvar_rs: rs number by clinvar
43 clinvar_clnsig: clinical significance by clinvar 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 7 - histocompatibility. A negative score means the score is for the ref allele"
44 clinvar_trait: the trait/disease the clinvar_clnsig referring to
45 clinvar_golden_stars: ClinVar Review Status summary 0 - no assertion criteria provided, 1 - criteria provided, single submitter, 2 - criteria provided, multiple submitters, no conflicts, 3 - reviewed by expert panel, 4 - practice guideline"
46 GTEx_V6_gene: Ensembl gene ID of the eQTL associated with
47 GTEx_V6_tissue: the tissue expression data in which the eQTL was detected
48 1000G_strict_masked: whether the site is within the 1000G strict masked region Y (Yes) or N (No), Y means generally good mapping quality"
49 RepeatMasker_masked: whether the site is masked by RepeatMasker Y (Yes) or N (No), Y means generally lower mapping quality"
50 Ancestral_allele: Ancestral allele (based on the EPO pipeline). The following comes from its original README file
51 phyloP46way_primate: a conservation score based on 46way alignment primate set, the higher the more conservative"
52 phyloP46way_primate_rankscore: the rank of the phyloP46way_primate score among all phyloP46way_primate scores in genome
53 phyloP20way_mammalian: a conservation score based on 20way alignment mammalian set, the higher the more conservative"
54 phyloP20way_mammalian_rankscore: the rank of the phyloP20way_mammalian score among all phyloP20way_mammalian scores in genome
55 phyloP100way_vertebrate: a conservation score based on 100way alignment vertebrate set, the higher the more conservative"
56 phyloP100way_vertebrate_rankscore: the rank of the phyloP100way_vertebrate score among all phyloP100way_vertebrate scores in genome
57 phastCons46way_primate: a conservation score based on 46way alignment primate set, the higher the more conservative"
58 phastCons46way_primate_rankscore: the rank of the phastCons46way_primate score among all phastCons46way_primate scores in genome
59 phastCons20way_mammalian: a conservation score based on 20way alignment mammalian set, the higher the more conservative"
60 phastCons20way_mammalian_rankscore: the rank of the phastCons20way_mammalian score among all phastCons20way_mammalian scores in genome
61 phastCons100way_vertebrate: a conservation score based on 100way alignment vertebrate set, the higher the more conservative"
62 phastCons100way_vertebrate_rankscore: the rank of the phastCons100way_vertebrate score among all phastCons100way_vertebrate scores in genome
63 GERP_NR: GERP++ neutral rate
64 GERP_RS: GERP++ RS score, the larger the score, the more conserved the site"
65 GERP_RS_rankscore: the rank of the GERP_RS score among all GERP_RS scores in genome
66 SiPhy_29way_logOdds: SiPhy score based on 29 mammals genomes. The larger the score, the more conserved the site"
67 SiPhy_29way_logOdds_rankscore: the rank of the SiPhy_29way_logOdds score among all SiPhy_29way_logOdds scores in genome
68 integrated_fitCons_score: fitCons scores (i6) based on function evidence from multiple cell types, the higher the score the more potential for interesting genomic function"
69 integrated_fitCons_rankscore: rank of the integrated_fitCons_score among all integrated_fitCons_scores in genome
70 integrated_confidence_value: confidence value for the integrated_fitCons_score
71 GM12878_fitCons_score: fitCons scores (gm) based on function evidence from the GM12878 cell type, the higher the score the more potential for interesting genomic function"
72 GM12878_fitCons_rankscore: rank of the GM12878_fitCons_score among all GM12878_fitCons_scores in genome
73 GM12878_confidence_value: confidence value for the GM12878_fitCons_score
74 H1-hESC_fitCons_score: fitCons scores (h1) based on function evidence from the H1-hESC cell type, the higher the score the more potential for interesting genomic function"
75 H1-hESC_fitCons_rankscore: rank of the H1-hESC_fitCons_score among all H1-hESC_fitCons_scores in genome
76 H1-hESC_confidence_value: confidence value for the H1-hESC_fitCons_score
77 HUVEC_fitCons_score: fitCons scores (hu) based on function evidence from the HUVEC cell type, the higher the score the more potential for interesting genomic function"
78 HUVEC_fitCons_rankscore: rank of the HUVEC_fitCons_score among all HUVEC_fitCons_scores in genome
79 HUVEC_confidence_value: confidence value for the HUVEC_fitCons_score
80 GenoCanyon_score: a functional prediction score based on conservation and biochemical annotations using unsupervised statistical learning. (doi
81 GenoCanyon_rankscore: rank of the GenoCanyon_score among all GenoCanyon_scores in genome
82 1000Gp3_AC: Alternative allele counts in the whole 1000 genomes phase 3 (1000Gp3) data.
83 1000Gp3_AF: Alternative allele frequency in the whole 1000Gp3 data.
84 1000Gp3_AFR_AC: Alternative allele counts in the 1000Gp3 African descendent samples.
85 1000Gp3_AFR_AF: Alternative allele frequency in the 1000Gp3 African descendent samples.
86 1000Gp3_EUR_AC: Alternative allele counts in the 1000Gp3 European descendent samples.
87 1000Gp3_EUR_AF: Alternative allele frequency in the 1000Gp3 European descendent samples.
88 1000Gp3_AMR_AC: Alternative allele counts in the 1000Gp3 American descendent samples.
89 1000Gp3_AMR_AF: Alternative allele frequency in the 1000Gp3 American descendent samples.
90 1000Gp3_EAS_AC: Alternative allele counts in the 1000Gp3 East Asian descendent samples.
91 1000Gp3_EAS_AF: Alternative allele frequency in the 1000Gp3 East Asian descendent samples.
92 1000Gp3_SAS_AC: Alternative allele counts in the 1000Gp3 South Asian descendent samples.
93 1000Gp3_SAS_AF: Alternative allele frequency in the 1000Gp3 South Asian descendent samples.
94 UK10K_AC: Alternative allele count in called genotypes in UK10K cohorts.
95 UK10K_AN: Total allele count in called genotypes in UK10K cohorts.
96 UK10K_AF: Alternative allele frequency in called genotypes in UK10K cohorts.
97 TWINSUK_AC: Alternative allele count in called genotypes in UK10K TWINSUK cohort.
98 TWINSUK_AN: Total allele count in called genotypes in UK10K TWINSUK cohort.
99 TWINSUK_AF: Alternative allele frequency in called genotypes in UK10K TWINSUK cohort.
100 ALSPAC_AC: Alternative allele count in called genotypes in UK10K TWINSUK cohort.
101 ALSPAC_AN: Total allele count in called genotypes in UK10K TWINSUK cohort.
102 ALSPAC_AF: Alternative allele frequency in called genotypes in UK10K TWINSUK cohort.
103 RegulomeDB_motif: motif the SNP resides (from RegulomeDB)
104 RegulomeDB_score: categorical score from RegulomeDB. The smaller, the more likely the SNP affects binding"
105 Motif_breaking: whether break a known motif (in-house script)
106 network_hub: whether the target gene is a network hub based on funseq-0.1
107 ENCODE_annotated: whether annotated by ENCODE based on funseq-0.1
108 sensitive: whether defined as sensitive region based on funseq-0.1
109 ultra_sensitive: whether defined as ultra-sensitive region based funseq-0.1
110 target_gene: target gene (for promoter, enhancer, etc.) based on funseq-0.1"
111 funseq_noncoding_score: funseq-like noncoding score range 0-6, each of the previous 5 columns contribute 1 if ""YES"", or 0 if ""NO""; the column Motif_breaking contribute 1 if it is not a ""."""
112 funseq2_noncoding_score: funseq2 noncoding score range 0-5.4 a weighted score designed for damaging prediction of cancer somatic SNPs
113 funseq2_noncoding_rankscore: the rank of the funseq2_noncoding_score among all funseq2_noncoding_scores in genome
114 CADD_raw: CADD raw score, the larger the number the more likely damaging"
115 CADD_phred: CADD phred-like score, ranges 1-99, the larger the number the more likely damaging; score >10 means the variant in the top 10% (0.1) among the total 8.6 billion possible SNVs, >20 means in the top 1%, >30 means in the top 0.1%, etc. CADD suggests a cutoff between 10 and 20 (e.g. 15)"
116 CADD_raw_rankscore: the rank of the CADD_raw score among all CADD_raw scores in genome
117 DANN_score: DANN is a functional prediction score retrained based on the training data of CADD using deep neural network. Scores range from 0 to 1. A larger number indicate a higher probability to be damaging. More information of this score can be found in doi
118 DANN_rank_score: rank of the DANN_score among all DANN_scores
119 fathmm-MKL_non-coding_score: fathmm-MKL non-coding prediction probability, the larger the number the more likely damaging; the threshold separating deleterious prediction and neutral prediction is 0.5."
120 fathmm-MKL_non-coding_rankscore: the rank of the fathmm-MKL_non-coding_score among all fathmm-MKL_non-coding_scores in genome
121 fathmm-MKL_non-coding_pred: If a fathmm-MKL_non-coding_score is >0.5 the corresponding nsSNV is predicted as ""D(AMAGING)""; otherwise it is predicted as ""N(EUTRAL)""."
122 fathmm-MKL_non-coding_group: fathmm-MKL non-coding group, the feature group used for the non-coding prediction "
123 fathmm-MKL_coding_score: fathmm-MKL coding prediction probability, the larger the number the more likely damaging the threshold separating deleterious prediction and neutral prediction is 0.5."
124 fathmm-MKL_coding_rankscore: the rank of the fathmm-MKL_coding_score among all fathmm-MKL_coding_scores in genome
125 fathmm-MKL_coding_pred: If a fathmm-MKL_coding_score is >0.5 the corresponding nsSNV is predicted as ""D(AMAGING)""; otherwise it is predicted as ""N(EUTRAL)""."
126 fathmm-MKL_coding_group: fathmm-MKL coding group, the feature group used for the coding prediction."
127 Eigen_coding_or_noncoding: Whether the Eigen and EigenPC scores are based on coding model or noncoding model
128 Eigen-raw: Eigen score for coding SNVs. A functional prediction score based on conservation, allele frequencies, and deleteriousness prediction using an unsupervised learning method (doi"
129 Eigen-phred: Eigen-raw score in phred scale.
130 Eigen-PC-raw: Eigen PC score for genome-wide SNVs. A functional prediction score based on conservation, allele frequencies, deleteriousness prediction (for missense SNVs) and epigenomic signals (for synonymous and non-coding SNVs) using an unsupervised learning method (doi"
131 Eigen-PC-phred: Eigen-PC-raw score in phred scale.
132 M_ref_raw_score: a list of predicted scores correspond to miRNA-target pairs predicted by miRanda that overlap with this locus. Separated by ';'.
133 M_ref_raw_miR: a list of mature miRNA names correspond to each of the scores in the M_ref_raw_score field. Separated by ';'.
134 M_ref_raw_gene: the Ensembl transcript ID corresponds to the M_ref_raw_score.
135 M_ref_exp_cor_tumo: For each miRNA-gene pair that overlaps this variant predicted by miRanda, a list of the correlation for their expression within 15 TCGA tumor tissues was presented."
136 M_ref_cor_tis_tumo: A list of tumor tissue names where the previous expression correlation values were calculated in.
137 M_ref_exp_cor_norm: For each miRNA-gene pair that overlaps this variant predicted by miRanda, a list of the correlation for their expression within 15 TCGA normal tissues was presented."
138 M_ref_cor_tis_norm: A list of normal tissue names where the previous expression correlation values were calculated in.
139 M_ref_best_score: the best score in the M_ref_raw_score field. For miRanda, the best score is the miRNA-target pair that has the highest prediction score."
140 M_ref_best_miR: the miRNA corresponds to the M_ref_best_score.
141 M_ref_best_gene: the Ensembl transcript ID corresponds to the M_ref_best_score.
142 M_ref_worst_score: the worst score in the M_ref_raw_score field. For miRanda, the worst score is the miRNA-target pair that has the lowest prediction score."
143 M_ref_worst_miR: the miRNA corresponds to the M_ref_worst_score.
144 M_ref_worst_gene: the Ensembl transcript ID corresponds to the M_ref_worst_score.
145 M_alt_raw_score: a list of predicted scores correspond to miRNA-target pairs that overlap with this locus after introducing the variant. Separated by ';'.
146 M_alt_raw_miR: a list of mature miRNA names correspond to each of the scores in the M_alt_raw_score field. Separated by ';'.
147 M_alt_raw_gene: a list of Ensembl transcript IDs correspond to each of the scores in the M_alt_raw_score field. Separated by ';'.
148 M_alt_exp_cor_tumo: For each miRNA-gene pair that overlaps this variant predicted by miRanda using SNV-induced 3'UTR, a list of the correlation for their expression within 15 TCGA tumor tissues was presented."
149 M_alt_cor_tis_tumo: A list of tumor tissue names where the previous expression correlation values were calculated in.
150 M_alt_exp_cor_norm: For each miRNA-gene pair that overlaps this variant predicted by miRanda using SNV-induced 3'UTR, a list of the correlation for their expression within 15 TCGA normal tissues was presented."
151 M_alt_cor_tis_norm: A list of normal tissue names where the previous expression correlation values were calculated in.
152 M_alt_best_score: the best score in the M_alt_raw_score field. For miRanda, the best score is the miRNA-target pair that has the highest prediction score."
153 M_alt_best_miR: the miRNA corresponds to the M_alt_best_score.
154 M_alt_best_gene: the Ensembl transcript ID corresponds to the M_alt_best_score.
155 M_alt_worst_score: the worst score in the M_alt_raw_score field. For miRanda, the worst score is the miRNA-target pair that has the lowest prediction score."
156 M_alt_worst_miR: the miRNA corresponds to the M_alt_worst_score.
157 M_alt_worst_gene: the Ensembl transcript ID corresponds to the M_alt_worst_score.
158 M_max_dif: the absolute value of the maximum potential difference between all the scores in M_ref_raw_score and M_alt_raw_score.
159 M_rankscore: the rank of the M_max_dif score among all M_max_dif socres within the same category (see M_cat).
160 M_max_gene: If the M_max_gene happened to be calculated between two miRNA-target pairs that are on the same transcript, this field shows the Ensembl transcript ID of the miRNA target. If the M_max_gene happened to be calculated using two miRNA-target pairs that belong to two different transcripts, this field shows as missing. "
161 M_cat: predicted functinoal category of this variant. 'S' stands for substitution of regulating miRNAs after introducing the variant; 'L' stands for loss of all regulating miRNAs after introducing the variant; 'G' stands for gain of novel regulating miRNAs when previously there was no miRNA regulation at this locus.
162 TS_ref_raw_score: a list of predicted scores correspond to miRNA-target pairs predicted by TargetScan that overlap with this locus. Separated by ';'.
163 TS_ref_raw_miR: a list of mature miRNA names correspond to each of the scores in the TS_ref_raw_score field. Separated by ';'.
164 TS_ref_raw_gene: a list of Ensembl transcript IDs correspond to each of the scores in the TS_ref_raw_score field. Separated by ';'.
165 TS_ref_exp_cor_tumo: For each miRNA-gene pair that overlaps this variant predicted by TargetScan, a list of the correlation for their expression within 15 TCGA tumor tissues was presented."
166 TS_ref_cor_tis_tumo: A list of tumor tissue names where the previous expression correlation values were calculated in.
167 TS_ref_exp_cor_norm: For each miRNA-gene pair that overlaps this variant predicted by TargetScan, a list of the correlation for their expression within 15 TCGA normal tissues was presented."
168 TS_ref_cor_tis_norm: A list of normal tissue names where the previous expression correlation values were calculated in.
169 TS_ref_best_score: the best score in the TS_ref_raw_score field. For TargetScan, the best score is the miRNA-target pair that has the largest negative prediction score."
170 TS_ref_best_miR: the miRNA corresponds to the TS_ref_best_score.
171 TS_ref_best_gene: the Ensembl transcript ID corresponds to the TS_ref_best_score.
172 TS_ref_worst_score: the worst score in the TS_ref_raw_score field. For TargetScan, the worst score is the miRNA-target pair that has the smallest negative prediction score."
173 TS_ref_worst_miR: the miRNA corresponds to the TS_ref_worst_score.
174 TS_ref_worst_gene: the Ensembl transcript ID corresponds to the TS_ref_worst_score.
175 TS_alt_raw_score: a list of predicted scores correspond to miRNA-target pairs that overlap with this locus after introducing the variant. Separated by ';'.
176 TS_alt_raw_miR: a list of mature miRNA names correspond to each of the scores in the TS_alt_raw_score field. Separated by ';'.
177 TS_alt_raw_gene: a list of Ensembl transcript IDs correspond to each of the scores in the TS_alt_raw_score field. Separated by ';'.
178 TS_alt_exp_cor_tumo: For each miRNA-gene pair that overlaps this variant predicted by TargetScan using SNV-induced 3'UTR, a list of the correlation for their expression within 15 TCGA tumor tissues was presented."
179 TS_alt_cor_tis_tumo: A list of tumor tissue names where the previous expression correlation values were calculated in.
180 TS_alt_exp_cor_norm: For each miRNA-gene pair that overlaps this variant predicted by TargetScan using SNV-induced 3'UTR, a list of the correlation for their expression within 15 TCGA normal tissues was presented."
181 TS_alt_cor_tis_norm: A list of normal tissue names where the previous expression correlation values were calculated in.
182 TS_alt_best_score: the best score in the TS_alt_raw_score field. For TargetScan, the best score is the miRNA-target pair that has the largest negative prediction score."
183 TS_alt_best_miR: the miRNA corresponds to the TS_alt_best_score.
184 TS_alt_best_gene: the Ensembl transcript ID corresponds to the TS_alt_best_score.
185 TS_alt_worst_score: the worst score in the TS_alt_raw_score field. For TargetScan, the worst score is the miRNA-target pair that has the smallest negativet prediction score."
186 TS_alt_worst_miR: the miRNA corresponds to the TS_alt_worst_score.
187 TS_alt_worst_gene: the Ensembl transcript ID corresponds to the TS_alt_worst_score.
188 TS_max_dif: the absolute value of the maximum potential difference between all the scores in TS_ref_raw_score and TS_alt_raw_score.
189 TS_rankscore: the rank of the TS_max_dif score among all TS_max_dif socres within the same category (see TS_cat).
190 TS_max_gene: If the TS_max_gene happened to be calculated between two miRNA-target pairs that are on the same transcript, this field shows the Ensembl transcript ID of the miRNA target. If the TS_max_gene happened to be calculated using two miRNA-target pairs that belong to two different transcripts, this field shows as missing. "
191 TS_cat: predicted functinoal category of this variant. 'S' stands for substitution of regulating miRNAs after introducing the variant; 'L' stands for loss of all regulating miRNAs after introducing the variant; 'G' stands for gain of novel regulating miRNAs when previously there was no miRNA regulation at this locus.
192 R_ref_raw_score: a list of predicted scores correspond to miRNA-target pairs predicted by RNAhybrid that overlap with this locus. Separated by ';'.
193 R_ref_raw_miR: a list of mature miRNA names correspond to each of the scores in the R_ref_raw_score field. Separated by ';'.
194 R_ref_raw_gene: a list of Ensembl transcript IDs correspond to each of the scores in the R_ref_raw_score field. Separated by ';'.
195 R_ref_exp_cor_tumo: For each miRNA-gene pair that overlaps this variant predicted by RNAhybrid, a list of the correlation for their expression within 15 TCGA tumor tissues was presented."
196 R_ref_cor_tis_tumo: A list of tumor tissue names where the previous expression correlation values were calculated in.
197 R_ref_exp_cor_norm: For each miRNA-gene pair that overlaps this variant predicted by RNAhybrid, a list of the correlation for their expression within 15 TCGA normal tissues was presented."
198 R_ref_cor_tis_norm: A list of normal tissue names where the previous expression correlation values were calculated in.
199 R_ref_best_score: the best score in the R_ref_raw_score field. For RNAhybrid, the best score is the miRNA-target pair that has the highest prediction score."
200 R_ref_best_miR: the miRNA corresponds to the R_ref_best_score.
201 R_ref_best_gene: the Ensembl transcript ID corresponds to the R_ref_best_score.
202 R_ref_worst_score: the worst score in the R_ref_raw_score field. For RNAhybrid, the worst score is the miRNA-target pair that has the lowest prediction score."
203 R_ref_worst_miR: the miRNA corresponds to the R_ref_worst_score.
204 R_ref_worst_gene: the Ensembl transcript ID corresponds to the R_ref_worst_score.
205 R_alt_raw_score: a list of predicted scores correspond to miRNA-target pairs that overlap with this locus after introducing the variant. Separated by ';'.
206 R_alt_raw_miR: a list of mature miRNA names correspond to each of the scores in the R_alt_raw_score field. Separated by ';'.
207 R_alt_raw_gene: a list of Ensembl transcript IDs correspond to each of the scores in the R_alt_raw_score field. Separated by ';'.
208 R_alt_exp_cor_tumo: For each miRNA-gene pair that overlaps this variant predicted by RNAhybrid using SNV-induced 3'UTR, a list of the correlation for their expression within 15 TCGA tumor tissues was presented."
209 R_alt_cor_tis_tumo: A list of tumor tissue names where the previous expression correlation values were calculated in.
210 R_alt_exp_cor_norm: For each miRNA-gene pair that overlaps this variant predicted by RNAhybrid using SNV-induced 3'UTR, a list of the correlation for their expression within 15 TCGA normal tissues was presented."
211 R_alt_cor_tis_norm: A list of normal tissue names where the previous expression correlation values were calculated in.
212 R_alt_best_score: the best score in the R_alt_raw_score field. For RNAhybrid, the best score is the miRNA-target pair that has the highest prediction score."
213 R_alt_best_miR: the miRNA corresponds to the R_alt_best_score.
214 R_alt_best_gene: the Ensembl transcript ID corresponds to the R_alt_best_score.
215 R_alt_worst_score: the worst score in the R_alt_raw_score field. For RNAhybrid, the worst score is the miRNA-target pair that has the lowest prediction score."
216 R_alt_worst_miR: the miRNA corresponds to the R_alt_worst_score.
217 R_alt_worst_gene: the Ensembl transcript ID corresponds to the R_alt_worst_score.
218 R_max_dif: the absolute value of the maximum potential difference between all the scores in R_ref_raw_score and R_alt_raw_score.
219 R_rankscore: the rank of the R_max_dif score among all R_max_dif socres within the same category (see R_cat).
220 R_max_gene: If the R_max_gene happened to be calculated between two miRNA-target pairs that are on the same transcript, this field shows the Ensembl transcript ID of the miRNA target. If the R_max_gene happened to be calculated using two miRNA-target pairs that belong to two different transcripts, this field shows as missing. "
221 R_cat: predicted functinoal category of this variant. 'S' stands for substitution of regulating miRNAs after introducing the variant; 'L' stands for loss of all regulating miRNAs after introducing the variant; 'G' stands for gain of novel regulating miRNAs when previously there was no miRNA regulation at this locus.