Reversal gene expression assessment for drug repurposing, a case study of glioblastoma

Table 3 Drugs identified in iLINCS with reversal gene expression signatures

		Cutoff	Signatures	Chemicals	Drugs
Signature Libraries	Cancer therapeutics response	< − 0.2	431	275	37
	LINCS Chemical perturbagen	< − 0.6	325	263	15
	Connectivity Map	< − 0.2	14	11	5
	DrugMatrix	< − 0.2	337	187	164
	Pharmacogenomics transcriptional	< − 0.2	377	26	126
	LINCS target proteomics	< − 0.2	33	32	3
Total		–	1517	794	350
Unique		–	–	726	119

The Cutoff column lists the Concordance score value used to filter the signatures with reversal gene expressions. A negative concordance denotes a possible reversal gene expression to GGEP. After the first-round screening using concordance < − 0.2 as a cutoff, we further strain the cutoff to < − 0.6 for the LINCS Chemical perturbagen library. This is based on the observation that much lower numbers of overlapped genes between its signatures and GGEP (approximately 10% of other signatures), which will increase false positive rate. The Signatures column lists the number of signatures identified in each signature library following the cutoffs. The Chemicals column lists the number of chemicals tested in these signatures. The Drugs column denotes the number of FDA-approved drugs identified accordingly. The row of Total denotes the numeric sum of signatures, chemicals, and drugs identified from all libraries, while the row of Unique lists the unique numbers of chemicals and drugs

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