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Dr. Son's Retracing the TNIK Discovery

A gene with zero papers.
How did it rank first?

Idiopathic pulmonary fibrosis has 4,591 candidate targets. Rank them by evidence and telomere genes rise to the top β€” and the ten seats below them are filled by targets that already have a drug.
TNIK, the one that actually became a drug, is not on that list at all. PubMed counts zero IPF papers for it at the time of discovery.
You rebuild the ranking in Python against three live APIs, then go to check causality with Perturb-seq β€” and meet the wrong cell.

🐍 Python🫁 IPF🎯 target discovery πŸ”Œ three live APIsπŸ“š PubMed🧬 Perturb-seqπŸ‡¬πŸ‡§ English
Start lesson 1 β†’

How you'll learn

πŸ”ŒThree live APIs

Open Targets, PubMed, Perturb-seq. All three wrappers keep the real contract.

πŸ”’You count the zero

You count TNIK's IPF papers on PubMed. At discovery time the answer is zero.

🎚️You turn one dial

Same data, same code, different winner. What decided it was not the arithmetic.

🧫You meet the wrong cell

You knock TNIK down and 11 genes move. The experiment was fine β€” the cell was wrong.

Full curriculum

01
이름 μ•ˆμ— β€œλͺ¨λ₯Έλ‹€β€ κ°€ λ“€μ–΄ μžˆλ‹€
νŠΉλ°œμ„± νμ„¬μœ μ¦ Β· Open Targets EFO_0000768 Β· μ—°κ΄€ ν‘œμ  4,591개
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02
이미 μžˆλŠ” μ•½ λ‘˜ β€” 늦좜 뿐 λ©ˆμΆ”μ§€ λͺ»ν•œλ‹€
INPULSIS 1,066λͺ… Β· ASCEND 555λͺ… Β· λ‘˜ λ‹€ 52μ£Ό
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03
ν‘œμ  ν•˜λ‚˜κ°€ λ‚˜λ¨Έμ§€ μ „λΆ€λ₯Ό μ •ν•œλ‹€
4,591 β†’ 1 Β· κ·Έ 사이에 μžˆλŠ” κ·œμΉ™λ“€
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04
무엇을 근거라고 λΆ€λ₯Ό 것인가 β€” 일곱 갈래
Open Targets datatypeScores Β· μœ μ „ν•™ Β· λ¬Έν—Œ Β· 동물 Β· λ°œν˜„ Β· 경둜 Β· μž„μƒ
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05
γ€μ‹€μŠ΅γ€‘ Open Targets λ₯Ό λ‘λ“œλ¦°λ‹€ β€” 후보 4,591κ°œμ— 쀄을 μ„Έμš΄λ‹€
GraphQL ν•œ 번 Β· μƒμœ„ 300개 Β· ν‘œμ  143개의 μžμ„Έν•œ 기둝
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06
μˆœμœ„κ°€ 이미 μ˜€μ—Όλ˜μ–΄ μžˆλ‹€ β€” 5λ“±λΆ€ν„° 15λ“±κΉŒμ§€μ˜ 정체
μƒμœ„ 30개 쀑 10κ°œκ°€ β€œμ΄λ―Έ 약이 μžˆμ–΄μ„œβ€ μ˜¬λΌμ™”λ‹€
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07
TNIK 은 이 λͺ©λ‘μ— μ—†λ‹€ β€” 300λ“± μ•ˆμ—λ„
TNIK 의 μ—°κ΄€ μ§ˆν™˜ 382개 Β· 그쀑 IPF λŠ” μ—†λ‹€
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08
γ€μ‹€μŠ΅γ€‘ μƒˆλ‘œμ›€μ„ μ„Όλ‹€ β€” TNIK 은 논문이 0νŽΈμ΄μ—ˆλ‹€
PubMed E-utilities Β· [tiab] Β· 2020λ…„μœΌλ‘œ 자λ₯Έ 이유
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09
γ€μ‹€μŠ΅γ€‘ μ†μž‘μ΄ ν•˜λ‚˜ β€” ν™•μ‹ κ³Ό μƒˆλ‘œμ›€μ„ κ³±ν•œλ‹€
같은 자료 Β· 같은 계산 Β· μ†μž‘μ΄ ν•˜λ‚˜λ‘œ κ°ˆλ¦¬λŠ” 1λ“±
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10
ν™˜μžλ₯Ό 봐도 μ•ˆ λ‚˜μ˜¨λ‹€ β€” λ°œν˜„ 자료의 μ‚¬κ°μ§€λŒ€
GEO μ‹œλ¦¬μ¦ˆ 4개 Β· IPF 102λͺ… λŒ€ 정상 40λͺ… Β· μƒμœ„ 600 μ•ˆμ— TNIK μ—†μŒ
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11
γ€μ‹€μŠ΅γ€‘ Perturb-seq API β€” κ»΄ 보고 무슨 일이 λ‚˜λŠ”μ§€ μ½λŠ”λ‹€
http://192.168.219.45:8500 Β· μ—”λ“œν¬μΈνŠΈ μ—¬μ„― Β· μœ μ „μž 11,526개
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12
γ€μ‹€μŠ΅γ€‘ μƒκ΄€μ—μ„œ 인과둜 β€” 후보λ₯Ό μ „λΆ€ κ»΄ λ³Έλ‹€
Open Targets μƒμœ„ 12개λ₯Ό Perturb-seq API 에 κ·ΈλŒ€λ‘œ λ„£λŠ”λ‹€
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13
TNIK μ΄λΌλŠ” μœ μ „μž β€” Wnt μœ„μ— 앉은 μΈμ‚°ν™”νš¨μ†Œ
TRAF2 and NCK interacting kinase Β· TCF7L2 Β· SMAD1 Thr-322 Β· ν˜•μ œ 아홉
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14
γ€μ‹€μŠ΅γ€‘ μž‘μ„ ν™ˆμ΄ μžˆλŠ”κ°€ β€” μ—¬κΈ°μ„œ 1등이 νƒˆλ½ν•œλ‹€
Open Targets tractability Β· μ €λΆ„μž μ—¬λŸ μΉΈ
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15
γ€μ‹€μŠ΅γ€‘ TNIK 을 껐닀. 아무 일도 μ—†μ—ˆλ‹€
세포 1,082개 Β· λ…Ήλ‹€μš΄ βˆ’21.4 Β· 흔듀린 μœ μ „μž 4개
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16
침묡의 μ„Έ μ’…λ₯˜ β€” 세포가 κ³§ μ§ˆλ¬Έμ΄λ‹€
μŠ€ν¬λ¦°μ— μ—†μŒ 36 Β· λˆŒλ¦¬μ§€ μ•ŠμŒ 21 Β· λˆŒλ ΈλŠ”λ° μ‘°μš©ν•¨
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17
이 슀크린이 μ‹€μ œλ‘œ λ‹΅ν•˜λŠ” 것 β€” 자료λ₯Ό νƒ“ν•˜μ§€ μ•ŠκΈ°
ν΄λŸ¬μŠ€ν„° 112개 Β· μžκ°€λ©΄μ—­ 17μ’… Β· μœ μ˜ν•œ μ—°κ΄€ 185건
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18
μ΄λ¦„μ—μ„œ λΆ„μžλ‘œ β€” 18κ°œμ›”, 그리고 78λͺ…
Ren F, et al. Nat Biotechnol 43:63–75 (2025) Β· NCT05154240
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19
γ€μ‹€μŠ΅γ€‘ 2a상 71λͺ… β€” +98.4 mL 을 μ–΄λ””κΉŒμ§€ 읽을 수 μžˆλ‚˜
Xu Z, Ren F, et al. Nat Med 31:2602–2610 (2025) Β· NCT05938920
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20
정리 β€” 말할 수 μžˆλŠ” 것과 μ—†λŠ” 것, 그리고 μ§„μ§œ API 둜
자료 μ…‹ Β· 계산 λ„· Β· 빈칸 λ‘˜
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