Using epigenomics data to predict gene expression in lung cancer

Li, Jeffery; Ching, Travers; Huang, Sijia; Garmire, Lana X

doi:10.1186/1471-2105-16-S5-S10

BMC Bioinformatics

Table 1 The list of all features considered prior to feature selection

From: Using epigenomics data to predict gene expression in lung cancer

	Average M value (Methylation)	Average Log Fold Change (Methylation)	Number of hypermethylated probes	Number of hypomethylated probes	Single nucleotide composition	Dinucleotide composition	Trinucleotide composition	Length of segment	Histone reads	Histone read comparisons (difference of reads/average of reads)	Conservation scores (PHASTCONS)
TSS 1500	TSS1500_avgMval	TSS1500_avglogFC	TSS1500_numHyper	TSS1500_numHypo	TSS1500_A	TSS1500_AA	TSS1500_AAA	--	TSS1500_S27	TSS1500_A27_minus_S27_divavg	TSS1500_vertebrate
TSS 200	TSS200_avgMval	TSS200_avglogFC	TSS200_numHyper	TSS200_numHypo	TSS200_A	TSS200_AA	TSS200_AAA	--	TSS200_S27	TSS200_A27_minus_S27_divavg	TSS200_vertebrate
UTR5	UTR5_avgMval	UTR5_avglogFC	UTR5_numHyper	UTR5_numHypo	UTR5_A	UTR5_AA	UTR5_AAA	UTR5_length	UTR5_S27	UTR5_A27_minus_S27_divavg	UTR5_vertebrate
First exon	first_exon_avgMval	first_exon_avglogFC	first_exon_numHyper	first_exon_numHypo	first_exon_A	first_exon_AA	first_exon_AAA	first_exon_length	first_exon_S27	first_exon_A27_minus_S27_divavg	first_exon_vertebrate
First Intron	first_intron_avgMval	first_intron_avglogFC	first_intron_numHyper	first_intron_numHypo	first_intron_A	first_intron_AA	first_intron_AAA	first_intron_length	first_intron_S27	first_intron_A27_minus_S27_divavg	first_intron_vertebrate
Exon Body	exon_avgMval	exon_avglogFC	exon_numHyper	exon_numHypo	exon_A	exon_AA	exon_AAA	exon_length	exon_S27	exon_A27_minus_S27_divavg	exon_vertebrate
Intron Body	intron_avgMval	intron_avglogFC	intron_numHyper	intron_numHypo	intron_A	intron_AA	intron_AAA	intron_length	intron_S27	intron_A27_minus_S27_divavg	intron_vertebrate
Coding Region (CDS)	CDS_avgMval	CDS_avglogFC	CDS_numHyper	CDS_numHypo	CDS_A	CDS_AA	CDS_AAA	CDS_length	CDS_S27	CDS_A27_minus_S27_divavg	CDS_vertebrate
Last Intron	last_intron_avgMval	last_intron_avglogFC	last_intron_numHyper	last_intron_numHypo	last_intron_A	last_intron_AA	last_intron_AAA	last_intron_length	last_intron_S27	last_intron_A27_minus_S27_divavg	last_intron_vertebrate
Last Exon	last_exon_avgMval	last_exon_avglogFC	last_exon_numHyper	last_exon_numHypo	last_exon_A	last_exon_AA	last_exon_AAA	last_exon_length	last_exon_S27	last_exon_A27_minus_S27_divavg	last_exon_vertebrate
UTR3	UTR3_avgMval	UTR3_avglogFC	UTR3_numHyper	UTR3_numHypo	UTR3_A	UTR3_AA	UTR3_AAA	UTR3_length	UTR3_S27	UTR3_A27_minus_S27_divavg	UTR3_vertebrate
Full Transcript	fullTranscript_avgMval	fullTranscript_avglogFC	fullTranscript_numHyper	fullTranscript_numHypo	fullTranscript_A	fullTranscript_AA	fullTranscript_AAA	fullTranscript_length	fullTranscript_S27	fullTranscript_A27_minus_S27_divavg	fullTranscript_vertebrate
Single Exon	single_exon_avgMval	single_exon_avglogFC	single_exon_numHyper	single_exon_numHypo	single_exon_A	single_exon_AA	single_exon_AAA	single_exon_length	single_exon_S27	single_exon_A27_minus_S27_divavg	single_exon_vertebrate
Single Intron	single_intron_avgMval	single_intron_avglogFC	single_intron_numHyper	single_intron_numHypo	single_intron_A	single_intron_AA	single_intron_AAA	single_intron_length	single_intron_S27	single_intron_A27_minus_S27_divavg	single_intron_vertebrate
Total Features	14	14	14	14	56	224	896	12	84	42	42	1412
Exon-exon junction distances:	Maximum distance to 5' end	Maximum distance to 3' end	Minimum distance to 5' end	Minimum distance to 3' end	Average distance to 5' end	Average Distance to 3' end
Hypermethylated	maxHyperTo5	maxHyperTo3	minHyperTo5	minHyperTo3	avgHyperTo5	avgHyperTo3
Hypomethylated	maxHypoTo5	maxHypoTo3	minHypoTo5	minHypoTo3	avgHypoTo5	avgHypoTo3
Total Features	2	2	2	2	2	2	12

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com