MAJIQ RT-PCR values
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Data corresponding to RT-PCR validations of cassette exon LSVs analyzed by MAJIQ in Vaquero-Garcia et al., 2016 (https://elifesciences.org/content/5/e11752). These LSVs are typically binary cassette exons. In some cases, MAJIQ detects additional junctions based on the Ensembl annotation DB or in the RNA-seq data. For this reason, we provide columns to explicitly specify the inclusive and exclusive junctions (i.e. cassette exon inclusion junction and cassette exon skipping junction) based on what was detected by RT-PCR in addition to ";" separated lists of all junctions and all quantifications output by MAJIQ for each LSV in addition to the 0-based index for the inclusive junction in those lists (in the last 4 columns).
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ColumnDescription
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LSV_IDunique LSV ID
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Chromosomechromosome
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Strandstrand
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IncJuncmm10 (cer vs. liv) or hg19 (stim vs. unstim) coordinates for inclusion junction
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ExcJuncmm10 (cer vs. liv) or hg19 (stim vs. unstim) coordinates for exclusion junction
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MAJIQ_incDPSIMAJIQ E(dPSI) value for inclusive junction for the comparison of the two groups
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MAJIQ_incPSI_[condition]MAJIQ E(PSI) value for inclusive junction for the given condition
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RTPCR_dPSI_[comparison]Average PSI for condition 1 - average PSI for condition 2 with n>=3 in each condition
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RTPCR_PSI_[condition]
Average PSI for given condition (n>=3 in every case) or PSI for given replicate for mouse tissues
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MAJIQ_incIndex
0-based index corresponding of the inclusive junction in the ";" separated lists of junction coordinates, dPSI values, and PSI values (see below)
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MAJIQ_allJuncs";" separated lists of junction coordinates (mm10 or hg19) for all junctions in an LSV.
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MAJIQ_allDPSI_[comparison]
";" separated lists of dPSI values for all junctions quantified in an LSV in given comparison
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MAJIQ_allPSI_[condition]";" separated lists of PSI values for all junctions quantified in an LSV in given condition
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README
Stim vs. Unstim
Cer vs. Liver