Discovery of Broad-Spectrum Antiviral Targets from Global Omics Data

Datasets:

Dataset SRR list at bottom of README

Human cell lines infected with Influenza virus ()
- Path to metadata table in this repo:
- Path to TPM table in this:
Human cell lines infected with SARS-CoV-2 ().
- Path to metadata table in this repo: results/covid/covid_experimental_metadata.csv
- Path to TPM table in this repo: results/covid/covid_experimental_metadata.csv
Mouse and monkey cell lines infected with Ebola virus ().
- Path to metadata table in this repo: results/ebola/ebola_experiment_metadata.csv
- Path to TPM tables in this repo: results/ebola/filtered_macfas.csv.gz results/ebola/filtered_macmul.csv.gz results/ebola/filtered_musmus.csv.gz

Methods

1. Process relevant human, monkey and mouse transcriptome data using in-house transcriptomic pipeline. Pipeline has multiple outputs, including transcripts per million (TPM) See below

2. Filter TPMs to remove all unexpressed genes using in house R pipeline.

Transcriptome Workflow description

Snakemake workflow.
Downloads SRR, maps it to human genome using Hisat2, counts the reads per feature using featurecount, and calculates TPMs.

Installation instruction for running snakemake workflow

This installation assumes you have conda installed and it is in your path.

Step 1: Clone the repo.

git clone https://github.com/bos-lab/human_response_path_viruses.git

Step 2: Update or Install the dependencies using following command

conda env update --file environment.yml --prune

Step 3: activate the conda environment

conda activate resp2virus-env

Step 4: Run

cd ANTIVIRAL-TARGETS
snakemake -p fcount_dir/SRS3059019_gene_fcount.tsv

Dataset SRR Lists

Human cell lines infected with Influenza virus

SRR7948444 SRR7948445 SRR7948446 SRR7948447 SRR7948452 SRR7948453 SRR7948454 SRR12606565 SRR12606566 SRR12606569 SRR12606570 SRR13161289 SRR13161290 SRR13161291 SRR13161303 SRR13161306 SRR13161309 SRR13319466_x SRR13319459 SRR13319464 SRR13319465 SRR13319460 SRR13319461 SRR13319466 SRR13319467 SRR13319462 SRR13319463 SRR13319468 SRR13319469 SRR13319476 SRR13319477 SRR13319486 SRR13319487 SRR13319478 SRR13319479 SRR13319488 SRR13319489 SRR13319480 SRR13319481 SRR13319490 SRR13319491 SRR13319482 SRR13319483 SRR13319492 SRR13319493 SRR13319484 SRR13319485 SRR13319494 SRR13319495 SRR13858418 SRR13858422 SRR13858423 SRR14272444 SRR14272445 SRR14272446 SRR14272447 SRR14272448 SRR14272449 SRR16676476 SRR16676479 SRR16676480 SRR16676484 SRR16676487 SRR16676490 SRR16676492 SRR16676518 SRR16676520 SRR16676522 SRR16676523 SRR16676526 SRR16676528 SRR16676529 SRR16676531 SRR16676534 SRR16676559 SRR16676563 SRR16676569 SRR16676571 SRR16676572 SRR16676575 SRR16676577 SRR16676579 SRR16676483 SRR16676562 SRR16676602 SRR16676455 SRR16676456 SRR16676457 SRR16676458 SRR16676459 SRR16676462 SRR16676468 SRR16676470 SRR16676472 SRR16676473 SRR16676474 SRR16676477 SRR16676478 SRR16676481 SRR16676485 SRR16676486 SRR16676488 SRR16676491 SRR16676493 SRR16676495 SRR16676497 SRR16676498 SRR16676500 SRR16676501 SRR16676509 SRR16676511 SRR16676512 SRR16676513 SRR16676521 SRR16676524 SRR16676525 SRR16676527 SRR16676530 SRR16676532 SRR16676533 SRR16676535 SRR16676536 SRR16676537 SRR16676538 SRR16676539 SRR16676540 SRR16676541 SRR16676542 SRR16676551 SRR16676552 SRR16676553 SRR16676554 SRR16676555 SRR16676556 SRR16676557 SRR16676560 SRR16676561 SRR16676564 SRR16676566 SRR16676567 SRR16676568 SRR16676570 SRR16676573 SRR16676574 SRR16676576 SRR16676578 SRR16676580 SRR16676581 SRR16676582 SRR16676583 SRR16676584 SRR16676585 SRR16676594 SRR16676595 SRR16676596 SRR16676597 SRR16676598 SRR16676599 SRR16676601 SRR16676603 SRR16676604 SRR16676605 SRR16676606 SRR16676607 SRR16676608 SRR16676609 SRR16676610 SRR16676611 SRR16676612 SRR16676613 SRR16676614 SRR16676558 SRR16676600 SRR16676482 SRR16676496 SRR16676499 SRR16676475 SRR16676514 SRR16676516 SRR16676489 SRR16676519 SRR16676565 SRR16676453 SRR16676461 SRR16676494 SRR16676515 SRR16676517 SRR16676454 SRR17319817 SRR17319820 SRR17319821 SRR17319825 SRR17319828 SRR17319829 SRR17319832 SRR17319833 SRR17319816 SRR17319824 SRR17468182 SRR17468183 SRR17468184 SRR17468186 SRR17468187 SRR17468188 SRR17468190 SRR17468191 SRR17468192 SRR18097076 SRR18097077 SRR18097078 SRR18097079 SRR18097080 SRR18097081 SRR18097082 SRR18097083 SRR18097084 SRR18097085 SRR18097086 SRR18097087 SRR18097088 SRR18097074 SRR18097075 SRR19663483 SRR19663484 SRR19663485 SRR19663486 SRR19663487 SRR19663488 SRR19663495 SRR19663497 SRR19663499 SRR19663500 SRR19663496 SRR19663498 CRR125934 CRR125935 CRR125936 CRR125937 CRR125938 CRR125939 CRR125940 CRR125941 CRR125942 CRR125943 CRR125944 CRR125945 CRR125946 CRR125947 CRR125948 CRR125949 CRR125950 CRR125951 CRR125952 CRR125953 CRR125954 CRR125955 CRR125956 CRR125957 CRR125958 CRR125959 CRR125960 CRR125961 CRR125962 CRR125963 CRR125964 CRR125965 CRR125966 CRR125967 CRR125968 CRR125969 CRR125970 CRR125971 CRR125972 CRR125973 CRR125974 CRR125975 CRR125977 CRR125978 CRR125979 CRR125980 CRR125981 CRR125983 CRR125984 CRR125985 CRR125986 CRR125987 CRR125989 CRR125990 CRR125991 CRR125992 CRR125993 CRR125994 CRR125995 CRR125996 CRR125997 CRR125998 CRR119890 CRR119891 CRR119892 CRR119893 CRR119894 CRR119895 CRR119896 CRR119897 CRR125445 CRR125446 SRR5677652 SRR5677654 SRR5677655 SRR5677656 SRR5677657 SRR5677658 SRR5677659 SRR5677660 SRR5677661 SRR10571655 SRR10571656 SRR10571657 SRR10571658 SRR10571659 SRR10571660 SRR10571662 SRR10571663 SRR10571664 SRR10571665 SRR10571719 SRR10571720 SRR10571721 SRR10571722 SRR10571723 SRR10571724 SRR10571725 SRR10571726 SRR10571727 SRR10571728 SRR10571730 SRR10571731 SRR10571732 SRR10571734 SRR10571735 SRR10571736 SRR10571737 SRR10571738 SRR10571739 SRR10571741 SRR10571742 SRR10571743 SRR10571744 SRR10571752 SRR10571753 SRR10571754 SRR10571755 SRR10571757 SRR7638277 SRR7638278 SRR7638279 SRR7638280 SRR7638281 SRR7638282 SRR7638283 SRR7638284 SRR7638286 SRR7638287 SRR7638288 SRR7638289 SRR7638290 SRR7638291 SRR7638292 SRR7638293 SRR7638294 SRR7638295 SRR7638296 SRR7638297 SRR7788513 SRR7788514 SRR7788515 SRR7788516 SRR7788517 SRR7788518 SRR7788519 SRR7788520 SRR7788521 SRR7788522 SRR7788523 SRR7788524 SRR7788525 SRR7788526 SRR7788527 SRR7788528 SRR7788529 SRR7788530 SRR7788531 SRR7788532 SRR7788533 SRR7796663 SRR10903402 SRR10903401 SRR10971381 SRR11059940 SRR11059941 SRR11059942 SRR11059943 SRR11059944 SRR11059945 SRR11059947 SRR11092056 SRR11092057 SRR11092058 SRR11092059 SRR11092060 SRR11092061 SRR11092062 SRR11092063 SRR11092064 SRR11548428 SRR11548429 SRR11548430 SRR11548431 SRR11548432 SRR11548433 SRR11548424 SRR11548426 SRR11548427 SRR11924416 SRR11924417 SRR11924418 SRR12023944 SRR12023945 SRR12023946 SRR12023947 SRR12023948 SRR12363210 SRR12363211 SRR12363212 SRR12363213 SRR12363214 SRR12363215 SRR12540045 SRR12540046 SRR12540047 SRR12540048 SRR12540049 SRR12540050 SRR12540051 SRR12540052 SRR12540053 SRR12540054 SRR12540055 SRR12540056 SRR12540057 SRR12540059 SRR12540060 SRR12540061 SRR12588852 SRR12588853 SRR12588854 SRR12588855 SRR12588856 SRR12588857 SRR12588861 SRR12588862 SRR12588863 SRR12789543 SRR12789544 SRR12789545 SRR12789546 SRR12937416 SRR12937417 SRR12937418 SRR12937419 SRR12937420 SRR12937421 SRR12937422 SRR12937423 SRR12937424 SRR12937425 SRR13010451 SRR13010452 SRR13165885 SRR13165886 SRR13165888 SRR13165889 SRR13165890 SRR13491260 SRR13491261 SRR13491262 SRR13491263 SRR13491264 SRR13491265 SRR13491266 SRR13491267 SRR13491268 SRR13491269 SRR13491270 SRR13491271 SRR13491272 SRR13743905 SRR13743906 SRR13743907 SRR13743908 SRR14917145 SRR14917146 SRR14917147 SRR14917148 SRR14917153 SRR14917154 SRR14917155 SRR14917156 SRR15700512 SRR15700513 SRR15700514 SRR15700515 SRR15700516 SRR15700517 SRR15700518 SRR15700519 SRR15700520 SRR15700521 SRR15700538 SRR15700539 SRR15700540 SRR15700542 SRR15700543 SRR15700544 SRR15700545 SRR15700546 SRR15700547 SRR17155269 SRR17155270 SRR17155271 SRR17155272 SRR17155273 SRR17155274 SRR17155275 SRR17155276 SRR17155277 SRR17155278 SRR17155279 SRR17155280 SRR17843989 SRR17843990 SRR17843991 SRR13319458

Mouse and monkey cell lines infected with Ebola virus

Macaca Fascicularis

SRR5630527 SRR5630528 SRR5630529 SRR5630530 SRR5630531 SRR5630532 SRR5630533 SRR5630534 SRR5630535 SRR5630536 SRR5630548 SRR5630549 SRR5630550 SRR5630551 SRR5630552 SRR5630553 SRR5630554 SRR5630555 SRR5630557 SRR5630558 SRR5630559 SRR5630560 SRR5630561 SRR5630562 SRR5630563 SRR5630564 SRR5630565 SRR5630566 SRR5630567

Macaca Mulatta

SRR7310674 SRR7310675 SRR7310676 SRR7310677 SRR7310678 SRR7310679 SRR7310680 SRR7310681 SRR7310682 SRR7310683 SRR7310684 SRR7310685 SRR7310686 SRR7310687 SRR7310688 SRR7310689 SRR7310690 SRR7310691 SRR7310692 SRR7310693 SRR7310694 SRR7310695 SRR7310696 SRR7310697 SRR7310698 SRR7310699 SRR7310700 SRR7310701 SRR7310702 SRR7310703 SRR7310704 SRR7310705 SRR7310706 SRR7310707 SRR7310708 SRR7310709 SRR7310710 SRR7310711 SRR7310712 SRR7310713 SRR7310714 SRR7310715 SRR7310716 SRR7310717 SRR7310718 SRR7310719 SRR7310720 SRR7310721 SRR7310722 SRR7310723 SRR7310724 SRR7310725 SRR7310726 SRR7310727 SRR7310728 SRR7310729 SRR7310730 SRR7310732 SRR7310733 SRR7310734 SRR7310735 SRR7310736 SRR7310738 SRR7310739 SRR7310740 SRR7310741 SRR7310742 SRR7310743 SRR7310745 SRR7310746 SRR7310747 SRR7310748 SRR7310749 SRR7310750 SRR7310751 SRR7310753 SRR7310754 SRR7310755 SRR7310756 SRR7310757 SRR7310758 SRR7310760 SRR7310761 SRR7310762 SRR7310763 SRR7310764 SRR7310766 SRR7310767 SRR7310768 SRR7310769 SRR7310770 SRR7310772 SRR7310773 SRR7310774 SRR7310775 SRR7310776 SRR7310777 SRR7310778 SRR7310779 SRR7310780 SRR7310781 SRR7310782 SRR7310783 SRR7310784 SRR7310785 SRR7310786 SRR7310787 SRR7310788 SRR7310789 SRR7310790 SRR7310791 SRR7310792 SRR7310793 SRR7310794 SRR7310795 SRR7310796 SRR7310797 SRR7310798 SRR7310799 SRR7310800 SRR7310801 SRR7310802 SRR7310803 SRR7310804 SRR7310805 SRR7310806 SRR7310807 SRR7310808 SRR7310809 SRR7310810 SRR7310811 SRR7310812 SRR7310813 SRR7310814 SRR7310815 SRR7310816 SRR7310817 SRR7310818 SRR7310819 SRR7310820 SRR7310821 SRR7310822 SRR7310823 SRR7310824 SRR7310825 SRR7310826 SRR7310827 SRR7310828 SRR7310829 SRR7310830 SRR7310831 SRR7310832 SRR7310833 SRR7310834 SRR7310835 SRR7310836 SRR7310837 SRR7310838 SRR7310839 SRR7310840 SRR7310841 SRR7310842 SRR7310843 SRR7310844 SRR7310845 SRR7310846 SRR7310847 SRR7310848 SRR7310849 SRR7310850 SRR7310851 SRR7310852 SRR7310853 SRR7310854 SRR7310855 SRR7310856 SRR7310857 SRR7310858 SRR7310859 SRR7310860 SRR7310861 SRR7310862 SRR7310863 SRR7310864 SRR7310865 SRR7310866 SRR7310867 SRR7310868 SRR7310869 SRR7310870 SRR7310871 SRR7310872 SRR7310873 SRR7310874 SRR7310875 SRR7310876 SRR7310877 SRR7310878 SRR7310879 SRR7310880 SRR7310881 SRR7310882 SRR7310883 SRR7310884 SRR7310885 SRR7310886 SRR7310887 SRR7310888 SRR7310889 SRR7310890 SRR7310891 SRR7310892 SRR7310893 SRR7310894 SRR7310895 SRR7310896 SRR7310897 SRR7310898 SRR7310899 SRR7310900 SRR7310901 SRR7310902 SRR7310903 SRR7310904 SRR7310905 SRR7310906 SRR7310907 SRR7310908 SRR7310909 SRR7310910 SRR7310911 SRR7310912 SRR7310913 SRR7310914 SRR7310915 SRR7310916 SRR7310917 SRR7310918 SRR7310919 SRR7310920 SRR7310921 SRR7310922 SRR7310923 SRR7310924 SRR7310925 SRR7310926 SRR7310927 SRR7310928 SRR7310929 SRR7310930 SRR7310931 SRR7310932 SRR7310933 SRR7310934 SRR7310935 SRR7310936 SRR7310937 SRR7310938 SRR7310939 SRR7310940 SRR7310941 SRR7310942 SRR7310943 SRR7310944 SRR7310945 SRR7310946 SRR7310947 SRR7310948 SRR7310949 SRR7310771

Mus musculus

SRR9003623 SRR9003565 SRR9003566 SRR9003567 SRR9003568 SRR9003569 SRR9003570 SRR9003571 SRR9003572 SRR9003573 SRR9003574 SRR9003575 SRR9003576 SRR9003577 SRR9003578 SRR9003579 SRR9003580 SRR9003581 SRR9003582 SRR9003583 SRR9003584 SRR9003585 SRR9003586 SRR9003587 SRR9003588 SRR9003589 SRR9003590 SRR9003591 SRR9003592 SRR9003593 SRR9003594 SRR9003595 SRR9003596 SRR9003597 SRR9003598 SRR9003599 SRR9003600 SRR9003601 SRR9003602 SRR9003603 SRR9003604 SRR9003605 SRR9003606 SRR9003607 SRR9003608 SRR9003609 SRR9003610 SRR9003611 SRR9003612 SRR9003613 SRR9003614 SRR9003615 SRR9003616 SRR9003617 SRR9003618 SRR9003619 SRR9003620 SRR9003621 SRR9003622 SRR9003624 SRR9003625 SRR9003626 SRR9003627 SRR9003628 SRR9003629 SRR9003630 SRR9003631 SRR9003632 SRR9003633 SRR9003634 SRR9003635 SRR9003636 SRR9003637 SRR9003638 SRR9003639 SRR9003640 SRR9003641 SRR9003642 SRR9003643 SRR9003644 SRR9003645 SRR9003646 SRR9003647 SRR9003648 SRR9003649 SRR9003650 SRR9003651 SRR9003652 SRR9003653 SRR9003654 SRR9003655 SRR9003656 SRR9003657 SRR9003658 SRR9003659 SRR9003660 SRR9003661 SRR9003662 SRR9003663 SRR9003664 SRR9003665 SRR9003666 SRR9003667 SRR9003668 SRR9003669 SRR9003670 SRR9003671 SRR9003672 SRR9003673 SRR9003674 SRR9003675 SRR9003676 SRR9003677 SRR9003678 SRR9003679 SRR9003680 SRR9003681 SRR9003682 SRR9003683 SRR9003684 SRR9003685 SRR9003686 SRR9003687 SRR9003688 SRR9003689 SRR9003690 SRR9003691 SRR9003692 SRR9003693 SRR9003694 SRR9003695 SRR9003696 SRR9003697 SRR9003698 SRR9003699 SRR9003700 SRR9003701 SRR9003702 SRR9003703 SRR9003704 SRR9003705 SRR9003706 SRR9003707 SRR9003708 SRR9003709 SRR9003710 SRR9003711 SRR9003712 SRR9003713 SRR9003714 SRR9003715 SRR9003716 SRR9003717 SRR9003718 SRR9003719 SRR9003720 SRR9003721 SRR9003722 SRR9003723 SRR9003724 SRR9003725 SRR9003726 SRR9003727 SRR9003728 SRR9003729 SRR9003730 SRR9003731 SRR9003732 SRR9003733 SRR9003734 SRR9003735 SRR9003736 SRR9003737 SRR9003738 SRR9003739 SRR9003740 SRR9003741 SRR9003742 SRR9003743 SRR9003744 SRR9003745 SRR9003746 SRR9003747 SRR9003748 SRR9003749 SRR9003750 SRR9003751 SRR9003752 SRR9003753 SRR9003754 SRR9003755 SRR9003756 SRR9003757 SRR9003758 SRR9003759 SRR9003760 SRR9003761 SRR9003762 SRR9003763 SRR9003764 SRR9003765 SRR9003766 SRR9003767 SRR9003768 SRR9003769 SRR9003770 SRR9003771 SRR9003772 SRR9003773 SRR9003774 SRR9003775 SRR9003776 SRR9003777 SRR9003778 SRR9003779 SRR9003780 SRR9003781 SRR9003782 SRR9003783 SRR9003784 SRR9003785 SRR9003786 SRR9003787 SRR9003788 SRR9003789 SRR9003790 SRR9003791 SRR9003793 SRR9003794 SRR9003795 SRR9003796 SRR9003797 SRR9003798 SRR9003799 SRR9003800 SRR9003801 SRR9003802 SRR9003803 SRR9003804 SRR9003805 SRR9003806 SRR9003807 SRR9003808 SRR9003809 SRR9003810 SRR9003811 SRR9003812 SRR9003813 SRR9003814 SRR9003815 SRR9003816 SRR9003817 SRR9003818 SRR9003819 SRR9003820 SRR9003821 SRR9003822 SRR9003823 SRR9003824 SRR9003826 SRR9003827 SRR9003829 SRR9003830 SRR9003831 SRR9003832 SRR9003833 SRR9003834 SRR9003835 SRR9003836 SRR9003837 SRR9003838 SRR9003839 SRR9003840 SRR9003841 SRR9003842 SRR9003843 SRR9003844 SRR9003845 SRR9003846 SRR9003847 SRR9003848 SRR9003849 SRR9003850 SRR9003851 SRR9003852 SRR9003853 SRR9003854 SRR9003855 SRR9003856 SRR9003857 SRR9003858 SRR9003859 SRR9003860 SRR9003861 SRR9003862 SRR9003863 SRR9003864 SRR9003865 SRR9003866 SRR9003867 SRR9003868 SRR9003869 SRR9003870 SRR9003871 SRR9003872 SRR9003873 SRR9003874 SRR9003875 SRR9003877 SRR9003878 SRR9003879 SRR9003880 SRR9003881 SRR9003882 SRR9003883 SRR9003884 SRR9003885 SRR9003886 SRR9003887 SRR9003888 SRR9003889 SRR9003890 SRR9003891 SRR9003892 SRR9003893 SRR9003894 SRR9003895 SRR9003896 SRR9003897 SRR9003898 SRR9003899 SRR9003900 SRR9003901 SRR9003902 SRR9003903 SRR9003904 SRR9003905 SRR9003906 SRR9003907 SRR9003908 SRR9003909 SRR9003910 SRR9003911 SRR9003912 SRR9003913 SRR9003914 SRR9003915 SRR9003916 SRR9003917 SRR9003918 SRR9003919 SRR9003920 SRR9003921 SRR9003922 SRR9003923 SRR9003924 SRR9003925 SRR9003926 SRR9003927 SRR9003928 SRR9003929 SRR9003930 SRR9003931 SRR9003932 SRR9003933

bos-lab/ANTIVIRAL-TARGETS