Table 2.

Cells and genes from esophageal biopsies after post-processing and analysis

Biopsy		Cell counts		All overlapping genes		COSMIC genes p < 0.05 and K* > 1
PIDa	Histology	RNA	DNA	No. any p and K*	No. p < 0.05 and K* > 1	No.	Max K* (gene)
20	CARDb	249	342	6671	98	7	1.12 (MUC1)c
20	ESOd	181	339	7581	2	0	—
9	NDBEe	160	362	3783	35	4	1.01 (ERBB2)
14	NDBE	259	200	9213	8	0	—
16	NDBE	237	227	7217	0	0	—
6	LGDf	221	353	7818	58	0	—
19	LGD	354	317	8566	5	0	—
6	HGDg	189	312	8308	485	35	1.54 (ERBB2)
14	HGD	172	117	7282	2612	119	1.27 (CXCR4)
20	HGDh	233	339	7148	416	39	1.33 (PTPRC)
16	EACi	187	274	7713	244	20	1.46 (GNAS)

We measured the contribution of genomic mutations to transcriptomic changes by K^* index of phylogenetic signal⁴⁹. For each gene, the p-value was estimated by a one-sided random permutation test with 999 repetitions to test K^* index against the null hypothesis of the gene expression values being randomly distributed in the phylogeny (n = number of DNA cells per biopsy).

^aPatient identification number from the original study.

^bHealthy gastric cardia.

^cThe gene names are italicized according to the organism-specific formatting guidelines for humans.

^dHealthy esophagus.

^eNon-dysplastic Barrett’s esophagus.

^fLow-grade dysplastic Barrett’s esophagus.

^gHigh-grade dysplastic Barrett’s esophagus.

^hThe first of two HGD biopsies from this patient separated by at least 5 cm.

ⁱEsophageal adenocarcinoma.