TY - GEN
T1 - Statistical comparisons of chromosomal shape populations
AU - Soto, Carlos J.
AU - Zhao, Peiyao A.
AU - Klein, Kyle N.
AU - Gilbert, David M.
AU - Srivastava, Anuj
N1 - Funding Information:
This research was supported in part by the grant NIH R01 GM126558 and NSF CDS&E DMS 1953087. There were no conflicts of interest in this research.
Publisher Copyright:
© 2021 IEEE.
PY - 2021/4/13
Y1 - 2021/4/13
N2 - This paper develops statistical tools for testing differences in shapes of chromosomes resulting from certain gene knockouts (KO), specifically RIF1 gene KO (RKO) and the cohesin subunit RAD21 gene KO (CKO). It utilizes a two-sample test for comparing shapes of KO chromosomes with wild type (WT) at two levels: (1) Coarse shape analysis, where one compares shapes of full or large parts of chromosomes, and (2) Fine shape analysis, where chromosomes are first segmented into (TAD-based) pieces and then the corresponding pieces are compared across populations. The shape comparisons-coarse and fine-are based on an elastic shape metric for comparing shapes of 3D curves. The experiments show that the KO populations, RKO and CKO, have statistically significant differences from WT at both coarse and fine levels. Furthermore, this framework highlights local regions where these differences are most prominent.
AB - This paper develops statistical tools for testing differences in shapes of chromosomes resulting from certain gene knockouts (KO), specifically RIF1 gene KO (RKO) and the cohesin subunit RAD21 gene KO (CKO). It utilizes a two-sample test for comparing shapes of KO chromosomes with wild type (WT) at two levels: (1) Coarse shape analysis, where one compares shapes of full or large parts of chromosomes, and (2) Fine shape analysis, where chromosomes are first segmented into (TAD-based) pieces and then the corresponding pieces are compared across populations. The shape comparisons-coarse and fine-are based on an elastic shape metric for comparing shapes of 3D curves. The experiments show that the KO populations, RKO and CKO, have statistically significant differences from WT at both coarse and fine levels. Furthermore, this framework highlights local regions where these differences are most prominent.
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U2 - 10.1109/ISBI48211.2021.9433812
DO - 10.1109/ISBI48211.2021.9433812
M3 - Conference contribution
AN - SCOPUS:85107198345
T3 - Proceedings - International Symposium on Biomedical Imaging
SP - 788
EP - 791
BT - 2021 IEEE 18th International Symposium on Biomedical Imaging, ISBI 2021
PB - IEEE Computer Society
T2 - 18th IEEE International Symposium on Biomedical Imaging, ISBI 2021
Y2 - 13 April 2021 through 16 April 2021
ER -