TABLE 1.

Summary of the expanded human gene annotation and the numbers of differentially expressed genes identified

Gene biotypea	Annotation	No. of differentially expressed genes identified in cells infected with:
		Intact HIV			UV-inactivated HIV
		Total	12 hpi	24 hpi	Total	12 hpi	24 hpi
Coding	20,317	8,570	1,660	8,189	1,118	826	425
Intergenic	359	248	64	234	51	44	17
lncRNA	16,927	1,098	98	1,074	45	29	18
sncRNA	8,527	29	4	26	6	0	6
Pseudogene	14,138	1,144	107	1,115	96	27	74
Other	841	5	0	5	1	1	0
Total	61,109	11,094	1,933	10,643	1,317	927	540

^aGene biotype was based on the GENCODE classification. For lncRNA, processed_transcript, lincRNA,3prime_overlapping_ncrna, antisense, sense_intronic, sense_overlapping. For sncRNA, snRNA, snoRNA, misc_RNA, miRNA. For pseudogene, polymorphic_pseudogene, pseudogene, IG_V_pseudogene, TR_V_pseudogene. For “other,” IG_V_gene, TR_C_gene, TR_J_gene, TR_V_gene, rRNA.