Table 2.

Region-Specific Signatures of Human Airway Epithelium

Category	Gene Symbol, GO Identifier, or UniProt Keyword	Fold Enrichment*	FDR (BH)
Distal
Top five enriched genes†
Secretoglobin family 3A member 2	SCGB3A2	64.1	<10−18
Surfactant protein B	SFTPB	32.1	<10−25
Surfactant protein A2	SFTPA2	24.6	<10−20
LIM domain only 3 (rhombotin-like 2)	LMO3	11.1	<10−14
Matrix Gla protein	MGP	9.6	<10−13
Transcription factor–related‡
Forkhead box A2	FOXA2	3.9	<10−10
Mohawk homeobox	MKX	3.0	<10−11
Sex-determining region Y (SRY) box 9	SOX9	3.0	<10−16
GATA-binding protein 6	GATA6	2.7	<10−24
Aristaless related homeobox	ARX	2.3	<10−14
Top annotation categories§
Extracellular space	GO:0005615	4.1	<10−4
Extracellular region part	GO:0044421	3.1	<10−3
Secreted	KW-0964	2.6	<10−3
Disulfide bond	KW-01015	2.1	<10−3
Signal	KW-0732	2.0	<10−2
Proximal
Top five enriched genes†
Plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)	PKP1	10.8	<10−20
ATPase H+ transporting lysosomal 42kDa V1 subunit C2	ATP6V1C2	7.8	<10−16
Tumor protein p63	TP63	7.7	<10−24
Dystonin	DST	7.6	<10−21
Tenascin C	TNC	7.4	<10−21
Transcription factor–related‡
Tumor protein p63	TP63	7.7	<10−24
HOXB cluster antisense RNA 1	HOXB-AS1	5.6	<10−20
Snail family zinc finger 2	SNAI2	5.1	<10−24
Homeobox A1	HOXA1	4.7	<10−12
Homeobox B3	HOXB3	4.0	<10−09
Top annotation categories§
Epithelial cell differentiation	GO:0030855	6.4	<10−3
Epidermal development	GO:0008544	5.9	<10−3
Ectodermal development	GO:0007398	5.5	<10−3
Skeletal system development	GO:0001501	3.9	<10−2
Extracellular matrix	GO:0031012	3.7	<10−2

Definition of abbreviations: BH = Benjamini-Hochberg correction; FDR = false discovery rate; GO = Gene Ontology database; KW = keyword; UniProt = Universal Protein Resource.

Distal and proximal signatures are listed (see Tables E1 and E2 for complete gene lists).

^*Fold enrichment (for genes, fold change in the expression of a given gene in the signature region compared with its expression in the compared anatomic region; for categories, defined by Database for Annotation, Visualization and Integrated Discovery [DAVID]).

^†Top five genes (ranked on basis of fold enrichment) are listed.

^‡Top five genes coding for transcription factors or transcription factor–related regulatory transcripts (ranked on basis of fold enrichment).

^§Top five annotation categories identified by DAVID (GO or UniProt KW; ranked by fold enrichment); criteria: (1) P < 0.05 with three corrections—BH, Bonferroni, and FDR; and (2) enrichment: >5% signature genes in the category.