TY - JOUR
T1 - The statistical geometry of transcriptome divergence in cell-type evolution and cancer
AU - Liang, Cong
AU - Forrest, Alistair R. R.
AU - Wagner, Günter P.
AU - AUTHOR GROUP
AU - Alam, Intikhab
AU - Albanese, Davide
AU - Altschuler, Gabriel
AU - Andersson, Robin
AU - Arakawa, Takahiro
AU - Archer, John
AU - Arner, Erik
AU - Arner, Peter
AU - Babina, Magda
AU - Baillie, Kenneth
AU - Bajic, Vladmir
AU - Baker, Sarah
AU - Balic, Adam
AU - Balwierz, Piotr
AU - Beckhouse, Anthony
AU - Bertin, Nicolas
AU - Blake, Judith A.
AU - Blumenthal, Antje
AU - Bodega, Beatrice
AU - Bonetti, Alessandro
AU - Briggs, James
AU - Brombacher, Frank
AU - Burroughs, Max
AU - Califano, Andrea
AU - Cannistraci, Carlo
AU - Carbajo, Daniel
AU - Carninci, Piero
AU - Chen, Yun
AU - Chierici, Marco
AU - Ciani, Yari
AU - Clevers, Hans
AU - Dalla, Emiliano
AU - Daub, Carsten
AU - Davis, Carrie
AU - de Hoon, Michiel
AU - de Lima Morais, David
AU - Dermar, Michael
AU - Diehl, Alexander
AU - Dimont, Emmanuel
AU - Dohl, Taeko
AU - Drabros, Finn
AU - Edge, Albert
AU - Edinger, Matthias
AU - Ekwall, Karl
AU - Endoh, Mitsuhiro
AU - Enomoto, Hideki
AU - Geijtenbeek, Teunis B. H.
PY - 2015
Y1 - 2015
N2 - In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination
AB - In evolution, body plan complexity increases due to an increase in the number of individualized cell types. Yet, there is very little understanding of the mechanisms that produce this form of organismal complexity. One model for the origin of novel cell types is the sister cell-type model. According to this model, each cell type arises together with a sister cell type through specialization from an ancestral cell type. A key prediction of the sister cell-type model is that gene expression profiles of cell types exhibit tree structure. Here we present a statistical model for detecting tree structure in transcriptomic data and apply it to transcriptomes from ENCODE and FANTOM5. We show that transcriptomes of normal cells harbour substantial amounts of hierarchical structure. In contrast, cancer cell lines have less tree structure, suggesting that the emergence of cancer cells follows different principles from that of evolutionary cell-type origination
U2 - https://doi.org/10.1038/ncomms7066
DO - https://doi.org/10.1038/ncomms7066
M3 - Article
C2 - 25585899
SN - 2041-1723
VL - 6
SP - 6066
JO - Nature communications
JF - Nature communications
ER -