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(ESI) for Integrative Biology. This Journal Is © the Royal Society of Chemistry 2017 Electronic Supplementary Material (ESI) for Integrative Biology. This journal is © The Royal Society of Chemistry 2017 Table 1 Enriched GO terms with p-value ≤ 0.05 corresponding to the over-expressed genes upon perturbation with the lung-toxic compounds. Terms with corrected p-value less than 0.001 are shown in bold. GO:0043067 regulation of programmed GO:0010941 regulation of cell death cell death GO:0042981 regulation of apoptosis GO:0010033 response to organic sub- stance GO:0043068 positive regulation of pro- GO:0010942 positive regulation of cell grammed cell death death GO:0006357 regulation of transcription GO:0043065 positive regulation of apop- from RNA polymerase II promoter tosis GO:0010035 response to inorganic sub- GO:0043066 negative regulation of stance apoptosis GO:0043069 negative regulation of pro- GO:0060548 negative regulation of cell death grammed cell death GO:0016044 membrane organization GO:0042592 homeostatic process GO:0010629 negative regulation of gene ex- GO:0001568 blood vessel development pression GO:0051172 negative regulation of nitrogen GO:0006468 protein amino acid phosphoryla- compound metabolic process tion GO:0070482 response to oxygen levels GO:0045892 negative regulation of transcrip- tion, DNA-dependent GO:0001944 vasculature development GO:0046907 intracellular transport GO:0008202 steroid metabolic process GO:0045934 negative regulation of nucle- obase, nucleoside, nucleotide and nucleic acid metabolic process GO:0006917 induction of apoptosis GO:0016481 negative regulation of transcrip- tion GO:0016125 sterol metabolic process GO:0012502 induction of programmed cell death GO:0001666 response to hypoxia GO:0051253 negative regulation of RNA metabolic process GO:0008203 cholesterol metabolic process GO:0010551 regulation of specific transcrip- tion from RNA polymerase II promoter 1 Table 2 Enriched GO terms with p-value ≤ 0.05 corresponding to the under-expressed genes upon perturbation with the lung-toxic compounds. Terms with corrected p-value less than 0.001 are shown in bold. GO:0022403 cell cycle phase GO:0022402 cell cycle process GO:0000278 mitotic cell cycle GO:0007049 cell cycle GO:0000279 M phase GO:0046907 intracellular transport GO:0048285 organelle fission GO:0051329 interphase of mitotic cell cycle GO:0043068 positive regulation of pro- GO:0010942 positive regulation of cell grammed cell death death GO:0051325 interphase GO:0051726 regulation of cell cycle GO:0043065 positive regulation of apop- GO:0000087 M phase of mitotic cell cy- tosis cle GO:0051301 cell division GO:0000280 nuclear division GO:0007067 mitosis GO:0033554 cellular response to stress GO:0032268 regulation of cellular protein GO:0043067 regulation of programmed cell metabolic process death GO:0010941 regulation of cell death GO:0006468 protein amino acid phosphoryla- tion GO:0042981 regulation of apoptosis GO:0006974 response to DNA damage stimu- lus GO:0006350 transcription GO:0080135 regulation of cellular response to stress GO:0010564 regulation of cell cycle process GO:0009057 macromolecule catabolic process GO:0032774 RNA biosynthetic process GO:0016310 phosphorylation GO:0051276 chromosome organization GO:0006357 regulation of transcription from RNA polymerase II promoter GO:0010605 negative regulation of macro- GO:0007059 chromosome segregation molecule metabolic process GO:0006913 nucleocytoplasmic transport 2 Table 3 Detailed results using the CMAP query tool for identifying drugs whose gene expression signatures have positive or negative correlation to the search query. As a search query the top 500 over- and under-expressed genes were used. The CMAP query tool scored every instance according to its correlation to the search query and sorted the output in descending order. For more details see https://www.broadinstitute.org/cmap rank batch cmap name dose cell score instance id 1 636 tamoxifen 7 µM MCF7 1 2212 2 626 thioridazine 10 µM MCF7 0.988 1655 3 725 thioridazine 10 µM MCF7 0.964 5227 4 636 terfenadine 8 µM MCF7 0.963 2227 5 730 metergoline 10 µM MCF7 0.96 5344 6 506 trifluoperazine 10 µM MCF7 0.956 1004 7 506 thioridazine 10 µM MCF7 0.944 1010 8 691 trimipramine 10 µM MCF7 0.943 4163 9 657 prenylamine 10 µM MCF7 0.942 2886 10 744 terfenadine 8 µM MCF7 0.941 6823 11 765 prochlorperazine 10 µM MCF7 0.926 6975 12 771 perhexiline 10 µM MCF7 0.925 7441 13 726 loperamide 8 µM MCF7 0.924 5267 14 505 calmidazolium 5 µM MCF7 0.924 906 15 736 pyrvinium 3 µM MCF7 0.92 5439 16 727 thioridazine 10 µM PC3 0.919 4454 17 731 mefloquine 10 µM PC3 0.919 5724 18 712 tonzonium bromide 7 µM PC3 0.919 4617 19 744 clomipramine 11 µM MCF7 0.917 6825 20 700 cloperastine 11 µM MCF7 0.917 4732 21 505 trifluoperazine 10 µM MCF7 0.914 910 22 755 fluspirilene 8 µM MCF7 0.914 6463 23 636 astemizole 9 µM MCF7 0.914 2211 24 699 alexidine 7 µM MCF7 0.913 4721 25 757 thioridazine 10 µM MCF7 0.913 5590 26 603 thioridazine 10 µM PC3 0.912 1230 27 755 tonzonium bromide 7 µM MCF7 0.912 6457 28 663 rescinnamine 6 µM MCF7 0.912 2785 29 744 astemizole 9 µM MCF7 0.911 6807 30 707 suloctidil 12 µM MCF7 0.909 5021 31 691 thioridazine 10 µM MCF7 0.909 4164 32 725 prochlorperazine 10 µM MCF7 0.908 5212 33 636 mefloquine 10 µM MCF7 0.908 2210 34 725 trifluoperazine 10 µM MCF7 0.906 5221 35 657 mometasone 8 µM MCF7 0.905 2896 3 36 727 trifluoperazine 10 µM PC3 0.9 4448 37 603 trifluoperazine 10 µM PC3 0.899 1224 38 506 fluphenazine 10 µM MCF7 0.895 1017 39 626 trifluoperazine 10 µM MCF7 0.895 1649 40 707 amoxapine 13 µM MCF7 0.894 4996 41 502 rottlerin 10 µM MCF7 0.892 941 42 755 phenoxybenzamine 12 µM MCF7 0.889 6451 43 502 resveratrol 10 µM MCF7 0.885 958 44 767 fluphenazine 10 µM MCF7 0.876 6954 45 707 fluspirilene 8 µM MCF7 0.874 5008 46 736 protriptyline 13 µM MCF7 0.871 5438 47 741 homochlorcyclizine 10 µM MCF7 0.871 5998 48 736 trifluoperazine 8 µM MCF7 0.87 5442 49 745 mefloquine 10 µM MCF7 0.87 6205 50 646 pimozide 9 µM MCF7 0.867 3178 51 728 astemizole 9 µM PC3 0.866 4471 52 743 pimozide 9 µM MCF7 0.865 6780 53 708 bepridil 10 µM MCF7 0.863 5674 54 506 prochlorperazine 10 µM MCF7 0.863 995 55 707 clomifene 7 µM MCF7 0.863 4994 56 502 pyrvinium 1 µM MCF7 0.863 978 57 736 propafenone 11 µM MCF7 0.862 5437 58 737 perhexiline 10 µM MCF7 0.859 5501 59 682 methylbenzethonium 9 µM PC3 0.858 3768 chloride 60 752 tetrandrine 6 µM MCF7 0.857 6082 61 747 proadifen 10 µM MCF7 0.857 7165 62 743 tamoxifen 7 µM MCF7 0.856 6768 63 637 antimycin A 7 µM MCF7 0.853 2261 64 632 niclosamide 12 µM MCF7 0.849 1498 65 771 trichostatin A 100 nM MCF7 0.849 7407 66 748 benzethonium chlo- 9 µM MCF7 0.848 7207 ride 67 505 ionomycin 2 µM MCF7 0.841 882 68 633 loperamide 8 µM MCF7 0.841 1533 69 633 perphenazine 10 µM MCF7 0.841 1540 70 726 phenoxybenzamine 12 µM MCF7 0.838 5248 71 771 nortriptyline 13 µM MCF7 0.837 7422 72 771 trifluoperazine 8 µM MCF7 0.837 7420 73 632 miconazole 10 µM MCF7 0.836 1477 74 758 loperamide 8 µM MCF7 0.833 5632 75 731 syrosingopine 6 µM PC3 0.832 5733 4 76 685 cloperastine 11 µM MCF7 0.832 3608 77 705 rescinnamine 6 µM MCF7 0.83 4386 78 757 prochlorperazine 10 µM MCF7 0.827 5575 79 655 amiodarone 6 µM MCF7 0.826 3296 80 751 methylbenzethonium 9 µM MCF7 0.826 6045 chloride 81 758 phenoxybenzamine 12 µM MCF7 0.825 5613 82 729 promethazine 12 µM MCF7 0.824 5317 83 681 cloperastine 11 µM PC3 0.824 3710 84 603 prochlorperazine 10 µM PC3 0.823 1215 85 757 15-delta 10 µM MCF7 0.823 5591 prostaglandin J2 86 636 ivermectin 5 µM MCF7 0.82 2213 87 737 prenylamine 10 µM MCF7 0.819 5489 88 718 prenylamine 10 µM PC3 0.819 5070 89 632 thioridazine 10 µM MCF7 0.817 1486 90 698 alexidine 7 µM PC3 0.815 7397 91 619 trifluoperazine 8 µM HL60 0.815 2389 92 736 amitriptyline 13 µM MCF7 0.815 5453 93 707 sulconazole 9 µM MCF7 0.815 4998 94 689 trimipramine 10 µM PC3 0.814 4083 95 727 prochlorperazine 10 µM PC3 0.813 4439 96 727 fluphenazine 10 µM PC3 0.813 4461 97 707 maprotiline 13 µM MCF7 0.813 5022 98 653 bepridil 10 µM MCF7 0.811 2629 99 711 methylbenzethonium 9 µM MCF7 0.811 3943 chloride 100 670 cloperastine 11 µM MCF7 0.811 3408 101 730 lynestrenol 14 µM MCF7 0.809 5355 102 741 nortriptyline 13 µM MCF7 0.809 6003 103 729 desipramine 13 µM MCF7 0.808 5292 104 616 mefloquine 10 µM PC3 0.808 2048 105 656 thiostrepton 2 µM MCF7 0.807 2823 106 603 fluphenazine 10 µM PC3 0.807 1237 107 772 Prestwick-559 8 µM MCF7 0.807 7462 108 711 promazine 12 µM MCF7 0.806 3927 109 706 miconazole 10 µM MCF7 0.804 4960 110 656 norcyclobenzaprine 15 µM MCF7 0.804 2830 111 752 benzethonium chlo- 9 µM MCF7 0.804 6070 ride 112 702 methylbenzethonium 9 µM PC3 0.802 4325 chloride 5 113 705 thiostrepton 2 µM MCF7 0.799 4385 114 735 hexetidine 12 µM MCF7 0.799 5420 115 729 puromycin 7 µM MCF7 0.798 5310 116 505 pararosaniline 10 µM MCF7 0.796 893 117 677 pyrvinium 3 µM MCF7 0.795 3518 118 694 norcyclobenzaprine 15 µM MCF7 0.794 4776 119 730 trichostatin A 100 nM MCF7 0.793 5336 120 689 thioridazine 10 µM PC3 0.791 4085 121 772 pimethixene 10 µM MCF7 0.791 7468 122 765 thioridazine 10 µM MCF7 0.788 6989 123 692 norcyclobenzaprine 15 µM PC3 0.787 4190 124 626 15-delta 10 µM MCF7 0.787 1656 prostaglandin J2 125 687 fenbendazole 13 µM MCF7 0.787 3888 126 505 celastrol 3 µM MCF7 0.786 887 127 682 promazine 12 µM PC3 0.786 3752 128 745 disulfiram 13 µM MCF7 0.786 6210 129 771 homochlorcyclizine 10 µM MCF7 0.785 7417 130 754 pyrvinium 3 µM PC3 0.784 6339 131 729 flupentixol 8 µM MCF7 0.784 5307 132 701 cloperastine 11 µM PC3 0.783 4271 133 771 econazole 9 µM MCF7 0.782 7427 134 505 5109870 25 µM MCF7 0.782 904 135 713 clioquinol 13 µM PC3 0.782 4663 136 731 thiethylperazine 6 µM PC3 0.782 5756
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