. 2018 Mar 9;34(16):2817–2825. doi: 10.1093/bioinformatics/bty133

Table 1.

A comparison between the results of three approaches: proposed, drug-disease, anti-correlation using IPF datasets (the top 10 drugs)

Proposed	Drug-disease	Anti-correlation	Proposed	Drug-disease	Anti-correlation
GSE24206-early			GSE24206-advanced
GSM1740570_saracatinib	GSM1746916_radicicol	GSM1746916_radicicol	GSM1740570_saracatinib	GSM1746916_radicicol	GSM1746916_radicicol
GSM1743214_nintedanib	GSM1746864_radicicol	GSM1746864_radicicol	GSM1743214_nintedanib	GSM1746864_radicicol	GSM1746864_radicicol
GSM1742836_celastrol	GSM1738326_mocetinostat^a	GSM1746893_radicicol	GSM1745714_buparlisib	GSM1738291_azacitidine^a	GSM1746893_radicicol
GSM1745714_buparlisib	GSM1738291_azacitidine^a	GSM1742836_celastrol	GSM1742836_celastrol	GSM1746893_radicicol	GSM1738290_azacitidine^a
GSM1742552_linifanib	GSM1738794_garcinol^a	GSM1738290_azacitidine^a	GSM1742552_linifanib	GSM1738772_ischemin	GSM1742836_celastrol
GSM1742850_nintedanib	GSM1745213_nilotinib^a	GSM1738291_azacitidine^a	GSM1740917_saracatinib	GSM1742836_celastrol	GSM1738291_azacitidine^a
GSM1740917_saracatinib	GSM1737397_quizartinib^a	GSM1745530_nilotinib^a	GSM1739549_saracatinib	GSM1737397_quizartinib^a	GSM1742552_linifanib
GSM1740731_CH5424802	GSM1743996_sirolimus^a	GSM1745213_nilotinib^a	GSM1742850_nintedanib	GSM1738326_mocetinostat^a	GSM1743996_sirolimus^a
GSM1743268_linifanib	GSM1742836_celastrol	GSM1742552_linifanib	GSM1740731_CH5424802	GSM1742718_sorafenib^a	GSM1742716_sorafenib^a
GSM1739549_saracatinib	GSM1746893_radicicol	GSM1742716_sorafenib^a	GSM1745213_nilotinib^a	GSM1746811_ruxolitinib^a	GSM1745530_nilotinib^a
GSE44723			GSE21369
GSM1741104_sunitinib^a	GSM1737411_NVP-BGT226	GSM1737409_NVP-BGT226	GSM1737700_rucaparib^a	GSM1737352_everolimus^a	GSM1737700_rucaparib^a
GSM1740080_sunitinib^a	GSM1743823_fostamatinib^a	GSM1737411_NVP-BGT226	GSM1740570_saracatinib	GSM1737699_rucaparib^a	GSM1737699_rucaparib^a
GSM1742552_linifanib	GSM1745509_NVP-BEZ235	GSM1740923_BI-2536^a	GSM1745714_buparlisib	GSM1737700_rucaparib^a	GSM1738767_decitabine^a
GSM1744393_gefitinib^a	GSM1737409_NVP-BGT226	GSM1740576_BI-2536^a	GSM1740731_CH5424802	GSM1738767_decitabine^a	GSM1740731_CH5424802
GSM1737353_everolimus^a	GSM1738100_tranylcypromine^a	GSM1745509_NVP-BEZ235	GSM1745213_nilotinib^a	GSM1746916_radicicol	GSM1737385_motesanib^a
GSM1742436_GDC-0941	GSM1741779_vorinostat^a	GSM1740570_saracatinib	GSM1742504_nintedanib	GSM1737385_motesanib^a	GSM1737624_entinostat
GSM1743268_linifanib	GSM1742856_canertinib^a	GSM1737412_NVP-BGT226	GSM1737448_idelalisib^a	GSM1742800_palbociclib^a	GSM1744048_imatinib^a
GSM1743214_nintedanib	GSM1742795_palbociclib^a	GSM1737353_everolimus^a	GSM1745530_nilotinib^a	GSM1737990_mocetinostat^a	GSM1737698_rucaparib^a
GSM1741743_sirolimus^a	GSM1739241_olaparib^a	GSM1745194_NVP-BEZ235	GSM1742836_celastrol	GSM1737443_idelalisib^a	GSM1738290_azacitidine^a
GSM1740570_saracatinib	GSM1740387_CH5424802	GSM1738308_entinostat	GSM1739679_dabrafenib^a	GSM1742836_celastrol	GSM1741754_sirolimus^a
LGRC-ILD			GSE1724
GSM1740570_saracatinib	GSM1738326_mocetinostat^a	GSM1738326_mocetinostat^a	GSM1741104_sunitinib^a	GSM1746800_nilotinib^a	GSM1746916_radicicol
GSM1739549_saracatinib	GSM1742795_palbociclib^a	GSM1737624_entinostat	GSM1740570_saracatinib	GSM1746916_radicicol	GSM1742552_linifanib
GSM1740917_saracatinib	GSM1737410_NVP-BGT226	GSM1739358_mocetinostat^a	GSM1739549_saracatinib	GSM1743953_linifanib	GSM1742836_celastrol
GSM1743214_nintedanib	GSM1741779_vorinostat^a	GSM1739435_belinostat^a	GSM1742552_linifanib	GSM1742836_celastrol	GSM1745213_nilotinib^a
GSM1743268_linifanib	GSM1737624_entinostat	GSM1741779_vorinostat^a	GSM1745714_buparlisib	GSM1745958_dasatinib^a	GSM1743268_linifanib
GSM1742552_linifanib	GSM1737411_NVP-BGT226	GSM1737410_NVP-BGT226	GSM1743268_linifanib	GSM1743268_linifanib	GSM1746864_radicicol
GSM1742504_nintedanib	GSM1739435_belinostat^a	GSM1746864_radicicol	GSM1740917_saracatinib	GSM1741215_veliparib^a	GSM1745626_vemurafenib
GSM1744170_GDC-0941	GSM1737409_NVP-BGT226	GSM1741767_vorinostat^a	GSM1740080_sunitinib^a	GSM1741184_regorafenib^a	GSM1743197_celastrol
GSM1745714_buparlisib	GSM1737455_vandetanib^a	GSM1737409_NVP-BGT226	GSM1742706_alvocidib	GSM1747067_mitoxantrone^a	GSM1744371_selumetinib
GSM1741265_saracatinib	GSM1738350_pracinostat	GSM1737642_mocetinostat^a	GSM1742850_nintedanib	GSM1741566_veliparib^a	GSM1746881_mitoxantrone^a

Note: The P-values for Wilcoxon rank sum test comparing the results of the proposed approach and drug-disease approach using datasets GSE24206-early, GSE24206-advanced, GSE44723, GSE21369, LGRC- ILD and GSE1724 are 0.02, 0.02, 0.01, 0.02, 0.01 and 0.01, respectively. Highlighted drugs are FDA-approved for the treatment of IPF. The proposed approach was the only one that was able to rank the FDA-approved Nintedanib in the top 10. In contrast, none of the existing approaches was able to retrieve the FDA-approved drug in any of these six datasets.

Drugs that are currently FDA-approved but for other indications.