Supplemental Table S1. Primers for SYBRGreen quantitative RT-PCR assays. Gene Accession Primer Sequence Length Start Stop Tm GC% GAPDH NM_002046.3 GAPDH F TCCTGTTCGACAGTCAGCCGCA 22 39 60 60.43 59.09 GAPDH R GCGCCCAATACGACCAAATCCGT 23 150 128 60.12 56.52 Exon junction 131/132 (reverse primer) on template NM_002046.3 DNAH6 NM_001370.1 DNAH6 F GGGCCTGGTGCTGCTTTGATGA 22 4690 4711 59.66 59.09% DNAH6 R TAGAGAGCTTTGCCGCTTTGGCG 23 4797 4775 60.06 56.52% Exon junction 4790/4791 (reverse primer) on template NM_001370.1 DNAH7 NM_018897.2 DNAH7 F TGCTGCATGAGCGGGCGATTA 21 9973 9993 59.25 57.14% DNAH7 R AGGAAGCCATGTACAAAGGTTGGCA 25 10073 10049 58.85 48.00% Exon junction 9989/9990 (forward primer) on template NM_018897.2 DNAI1 NM_012144.2 DNAI1 F AACAGATGTGCCTGCAGCTGGG 22 673 694 59.67 59.09 DNAI1 R TCTCGATCCCGGACAGGGTTGT 22 822 801 59.07 59.09 Exon junction 814/815 (reverse primer) on template NM_012144.2 RPGRIP1L NM_015272.2 RPGRIP1L F TCCCAAGGTTTCACAAGAAGGCAGT 25 3118 3142 58.5 48.00% RPGRIP1L R TGCCAAGCTTTGTTCTGCAAGCTGA 25 3238 3214 60.06 48.00% Exon junction 3124/3125 (forward primer) on template NM_015272.2 Supplemental Table S2. Transcripts that differentiate IPF/UIP from controls at 5%FDR Fold- p-value Change Transcript Gene p-value p-value p-value (IPF/UIP (IPF/UIP Cluster ID RefSeq Symbol gene_assignment (Age) (Gender) (Smoking) vs. C) vs. C) NM_001178008 // CBS // cystathionine-beta- 8070632 NM_001178008 CBS synthase // 21q22.3 // 875 /// NM_0000 0.456642 0.314761 0.418564 4.83E-36 -2.23 NM_003013 // SFRP2 // secreted frizzled- 8103254 NM_003013 SFRP2 related protein 2 // 4q31.3 // 6423 /// 0.625595 0.078456 0.339615 1.42E-30 6.96 NM_015374 // SUN2 // Sad1 and UNC84 8076137 NM_015374 SUN2 domain containing 2 // 22q13.1 // 25777 /// 0.74974 0.011049 0.67162 1.40E-29 -1.82 NM_002084 // GPX3 // glutathione peroxidase 3 (plasma) // 5q23 // 2878 /// 8109333 NM_002084 GPX3 ENST0 0.430133 0.002053 0.643244 1.22E-28 -2.74 NM_002563 // P2RY1 // purinergic receptor 8083447 NM_002563 P2RY1 P2Y, G-protein coupled, 1 // 3q25.2 // 0.615801 0.950295 0.365474 6.16E-27 -2.86 NM_001793 // CDH3 // cadherin 3, type 1, P- 7996819 NM_001793 CDH3 cadherin (placental) // 16q22.1 // 10 0.009559 0.448395 0.411104 3.75E-26 3.58 NM_022351 // NECAB1 // N-terminal EF- 8147244 NM_022351 NECAB1 hand calcium binding protein 1 // 8q21.3 // 0.685413 0.332522 0.739776 7.05E-25 -3.59 NM_001012334 // MDK // midkine (neurite 7939665 NM_001012334 MDK growth-promoting factor 2) // 11p11.2 // 0.27205 0.650887 0.781016 7.21E-25 1.93 NM_002340 // LSS // lanosterol synthase 8070961 NM_002340 LSS (2,3-oxidosqualene-lanosterol cyclase) / 0.737654 0.182236 0.844486 1.36E-24 -1.94 NM_021110 // COL14A1 // collagen, type 8148070 NM_021110 COL14A1 XIV, alpha 1 // 8q23 // 7373 /// ENST0000 0.354378 0.460841 0.952138 1.77E-24 4.09 NM_000680 // ADRA1A // adrenergic, alpha- 8149885 NM_000680 ADRA1A 1A-, receptor // 8p21.2 // 148 /// NM_0 0.014366 0.115339 0.623063 2.75E-24 -2.22 NM_004668 // MGAM // maltase- glucoamylase (alpha-glucosidase) // 7q34 // 8136662 NM_004668 MGAM 8972 // 0.163269 0.921797 0.789496 3.02E-24 -4.16 NM_198516 // GALNTL4 // UDP-N-acetyl- alpha-D-galactosamine:polypeptide N- 7946641 NM_198516 GALNTL4 acetylg 0.260153 0.750474 0.90351 3.66E-24 -2.18 NM_021135 // RPS6KA2 // ribosomal protein S6 kinase, 90kDa, polypeptide 2 // 8130739 NM_021135 RPS6KA2 6q2 0.462264 0.094697 0.938204 1.41E-23 -1.82 NM_014839 // LPPR4 // lipid phosphate 7903214 NM_014839 LPPR4 phosphatase-related protein type 4 // 1p21 0.526718 0.622418 0.134065 6.25E-23 2.45 NM_017680 // ASPN // asporin // 9q22 // 8162394 NM_017680 ASPN 54829 /// NM_001193335 // ASPN // aspori 0.008958 0.91816 0.0741792 6.94E-23 5.16 NM_004672 // MAP3K6 // mitogen- activated protein kinase kinase kinase 6 // 7914042 NM_004672 MAP3K6 1p36. 0.343731 0.916583 0.821909 1.40E-22 -1.88 NM_015310 // PSD3 // pleckstrin and Sec7 8149555 NM_015310 PSD3 domain containing 3 // 8p21.3 // 23362 0.132732 0.580459 0.238988 1.42E-22 1.93 NM_032532 // FNDC1 // fibronectin type III 8123104 NM_032532 FNDC1 domain containing 1 // 6q25 // 84624 0.824688 0.538236 0.390894 2.08E-22 2.96 NM_020440 // PTGFRN // prostaglandin F2 7904293 NM_020440 PTGFRN receptor negative regulator // 1p13.1 // 0.712214 0.131824 0.2651 7.52E-22 2.14 NM_006288 // THY1 // Thy-1 cell surface 7952268 NM_006288 THY1 antigen // 11q23.3 // 7070 /// ENST00000 0.177 0.186278 0.398847 3.78E-21 3.55 NM_013989 // DIO2 // deiodinase, iodothyronine, type II // 14q24.2-q24.3 // 7980485 NM_013989 DIO2 1734 0.41374 0.001194 0.136475 3.81E-21 2.54 NM_024551 // ADIPOR2 // adiponectin receptor 2 // 12p13.31 // 79602 /// 7953021 NM_024551 ADIPOR2 ENST0000 0.615955 0.085916 0.372758 3.82E-21 -1.82 NM_016286 // DCXR // dicarbonyl/L-xylulose 8019357 NM_016286 DCXR reductase // 17q25.3 // 51181 /// NM_ 0.0145 0.432558 0.847005 4.55E-21 -1.67 NM_033495 // KLHL13 // kelch-like 13 (Drosophila) // Xq23-q24 // 90293 /// 8174654 NM_033495 KLHL13 NM_00 0.39826 0.263702 0.991129 5.64E-21 2.51 NM_031935 // HMCN1 // hemicentin 1 // 1q25.3-q31.1 // 83872 /// 7908204 NM_031935 HMCN1 ENST00000271588 0.007176 0.964079 0.763295 7.13E-21 2.42 NM_206927 // SYTL2 // synaptotagmin-like 7950810 NM_206927 SYTL2 2 // 11q14 // 54843 /// NM_206928 // SY 0.037707 0.342637 0.783203 8.41E-21 1.97 NM_003749 // IRS2 // insulin receptor 7972745 NM_003749 IRS2 substrate 2 // 13q34 // 8660 /// ENST00000 0.952433 0.097443 0.249027 9.40E-21 -1.88 NM_181711 // GRASP // GRP1 (general 7955578 NM_181711 GRASP receptor for phosphoinositides 1)-associated 0.309603 0.262771 0.634118 9.96E-21 -2.50 NM_005621 // S100A12 // S100 calcium 7920238 NM_005621 S100A12 binding protein A12 // 1q21 // 6283 /// ENS 0.050753 0.718753 0.402793 1.08E-20 -3.83 NM_003637 // ITGA10 // integrin, alpha 10 7904761 NM_003637 ITGA10 // 1q21 // 8515 /// ENST00000369304 // 0.396106 0.127081 0.212834 1.25E-20 -2.37 NM_016206 // VGLL3 // vestigial like 3 8088979 NM_016206 VGLL3 (Drosophila) // 3p12.1 // 389136 /// ENST 0.002928 0.010553 0.256786 1.35E-20 -2.10 NM_013427 // ARHGAP6 // Rho GTPase 8171313 NM_013427 ARHGAP6 activating protein 6 // Xp22.3 // 395 /// NM_ 0.001126 0.701491 0.870062 2.06E-20 -2.01 NM_004887 // CXCL14 // chemokine (C-X-C 8114249 NM_004887 CXCL14 motif) ligand 14 // 5q31 // 9547 /// ENS 0.115706 0.827791 0.463199 2.37E-20 2.45 NM_024693 // ECHDC3 // enoyl CoA hydratase domain containing 3 // 10p14 // 7926152 NM_024693 ECHDC3 79746 0.723514 0.130592 0.694849 2.75E-20 -1.73 NM_032160 // DSEL // dermatan sulfate 8023727 NM_032160 DSEL epimerase-like // 18q22.1 // 92126 /// ENS 0.024499 0.100221 0.564341 2.99E-20 -1.92 NM_001080393 // GXYLT2 // glucoside 8080964 NM_001080393 GXYLT2 xylosyltransferase 2 // 3p13 // 727936 /// E 0.890374 0.505058 0.549978 3.11E-20 2.49 NM_000906 // NPR1 // natriuretic peptide 7905606 NM_000906 NPR1 receptor A/guanylate cyclase A (atriona 0.221305 0.043182 0.712389 3.50E-20 -2.44 NM_024850 // BTNL8 // butyrophilin-like 8 8116537 NM_024850 BTNL8 // 5q35.3 // 79908 /// NM_001040462 // 0.43025 0.197733 0.405111 4.14E-20 -1.71 NM_018398 // CACNA2D3 // calcium channel, voltage-dependent, alpha 2/delta 8080578 NM_018398 CACNA2D3 subun 0.060511 0.243001 0.0082213 4.59E-20 -1.67 NM_052917 // GALNT13 // UDP-N-acetyl- alpha-D-galactosamine:polypeptide N- 8045776 NM_052917 GALNT13 acetylg 0.017951 0.09348 0.157563 6.66E-20 -2.15 NM_144687 // NLRP12 // NLR family, pyrin 8039096 NM_144687 NLRP12 domain containing 12 // 19q13.42 // 916 0.057388 0.661991 0.929529 8.52E-20 -1.76 NM_181353 // ID1 // inhibitor of DNA 8061564 NM_181353 ID1 binding 1, dominant negative helix-loop-hel 0.516844 0.227374 0.163939 9.08E-20 -2.52 NM_152996 // ST6GALNAC3 // ST6 (alpha-N- 7902425 NM_152996 ST6GALNAC3acetyl-neuraminyl-2,3-beta-galactosyl-1, 0.15897 0.288073 0.832047 9.43E-20 -2.05 NM_005086 // SSPN // sarcospan (Kras oncogene-associated gene) // 12p11.2 // 7954481 NM_005086 SSPN 808 0.010514 0.743244 0.565015 9.75E-20 1.78 NM_015310 // PSD3 // pleckstrin and Sec7 8149551 NM_015310 PSD3 domain containing 3 // 8p21.3 // 23362 0.013523 0.927144 0.156792 1.18E-19 2.15 NM_001135181 // SLC5A9 // solute carrier 7901316 NM_001135181 SLC5A9 family 5 (sodium/glucose cotransporter) 0.011155 0.424205 0.0183648 1.38E-19 -2.01 NM_005824 // LRRC17 // leucine rich repeat 8135218 NM_005824 LRRC17 containing 17 // 7q22.1 // 10234 /// 0.79711 0.013604 0.737823 1.40E-19 2.79 NM_156039 // CSF3R // colony stimulating 7914950 NM_156039 CSF3R factor 3 receptor (granulocyte) // 1p35 0.118326 0.288053 0.690138 1.55E-19 -2.49 NM_019086 // VSIG10 // V-set and immunoglobulin domain containing 10 // 7966839 NM_019086 VSIG10 12q24.23 0.041268 0.010701 0.733545 1.69E-19 -1.61 NM_018945 // PDE7B // phosphodiesterase 8122222 NM_018945 PDE7B 7B // 6q23-q24 // 27115 /// ENST00000308 0.491208 0.809038 0.311159 1.79E-19 2.18 NM_016354 // SLCO4A1 // solute carrier 8063923 NM_016354 SLCO4A1 organic anion transporter family, member 0.169865 0.646993 0.136994 2.26E-19 -3.33 NM_203371 // FIBIN // fin bud initiation 7939052 NM_203371 FIBIN factor homolog (zebrafish) // 11p14.2 / 0.010942 0.001672 0.176034 2.36E-19 -2.75 NM_015419 // MXRA5 // matrix-remodelling 8171172 NM_015419 MXRA5 associated 5 // Xp22.33 // 25878 /// EN 0.870662 0.666444 0.375889 2.38E-19 2.50 NM_004779 // CNOT8 // CCR4-NOT transcription complex, subunit 8 // 5q31-q33 8109462 NM_004779 CNOT8 // 9 0.89724 0.05076 0.570686 2.56E-19 -1.56 NM_004734 // DCLK1 // doublecortin-like 7970954 NM_004734 DCLK1 kinase 1 // 13q13 // 9201 /// NM_0011954 0.668455 0.2099 0.93869 3.19E-19 2.82 NM_022470 // ZMAT3 //