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[์—ฐ์„ธ๋Œฟ’/๋ฏธ์ƒ๋ฌผ์‹คํ—˜๋ณด๊ณ ์„œ/A+]Cancer genomics data visualization & Analysis with UCSC Xena Browser

"[์—ฐ์„ธ๋Œฟ’/๋ฏธ์ƒ๋ฌผ์‹คํ—˜๋ณด๊ณ ์„œ/A+]Cancer genomics data visualization & Analysis with UCSC Xena Browser"์— ๋Œ€ํ•œ ๋‚ด์šฉ์ž…๋‹ˆ๋‹ค.
6 ํŽ˜์ด์งฟ’
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์ตœ์ดˆ๋“ฑ๋ก์ผ 2022.02.02 ์ตœ์ข…์ ฟ’์ž‘์ผ 2020.02
6P ๋ฏธ๋้ฉ๋ณด๊ธฐ
[์—ฐ์„ธ๋Œฟ’/๋ฏธ์ƒ๋ฌผ์‹คํ—˜๋ณด๊ณ ์„œ/A+]Cancer genomics data visualization & Analysis with UCSC Xena Browser
  • ๋ฏธ๋้ฉ๋ณด๊ธฐ

    ๋ชฉ์ฐจ

    1. Introduction
    2. Result
    3. Discussion
    4. Reference

    ๋ณธ๋ๅฉ๋‚ด์šฉ

    The purpose of this experiment was to use the UCSC Xena browser as a tool for cancer function genomics visualization and analysis. In todayโ€™s experiment we specifically used Xena to see the survival difference between two subtypes of a brain cancer called โ€˜Lower grade Gliomaโ€™. The two types of lower grade glioma are subtype A which is characterized by the loss of chromosome 1p& 19q and the subtype B which is characterized by mutations in TP53 and ATRX. It is said that the subtype A group has a better survival prognosis than the subtype B group. The Xena browser was used to create a Kaplan Meier plot to see the statistical significance between the survival differences between the two subtype groups.

    ์ฐธ๊ณ ์ž๋ฃŒ

    ยท Zhang, Chuang et al. โ€œComprehensive analysis of genes based on chr1p/19q co-deletion reveals a robust 4-gene prognostic signature for lower grade glioma.โ€ Cancer management and research vol. 11 4971-4984. 29 May. 2019
    ยท Tang J, Wu S, Liu H, Stratt R, Barak OG, Shiekhattar R, et al. A novel transcription regulatory complex containing death domain-associated protein and the ATR-X syndrome protein. J Biol Chem (2004) 279(19):20369โ€“77. doi:10.1074/jbc.M401321200
    ยท ATRX gene - Genetics Home Reference - NIH. (n.d.). Retrieved March 19, 2020, from https://ghr.nlm.nih.gov/gene/ATRX
  • Easy Ai ์š”์•ฝ

    ์ด ๋ฌธ์„œ๋Š” UCSC Xena ๋ธŒ๋ผ์šฐ์ €๋ฅผ ํ™œ์šฉํ•œ ์•” ์œ ์ „์ฒดํ•™ ๋ฐ์ดํ„ฐ ์‹œ๊ฐํ™” ๋ฐ ๋ถ„์„ ์‹คํ—˜ ๊ฒฐ๊ณผ๋ฅผ ์ž์„ธํžˆ ์„ค๋ช…ํ•˜๊ณ  ์žˆ๋‹ค. ์‹คํ—˜์—์„œ๋Š” ๋‚ฎ์€ ๋“ฑ๊ธ‰ ๊ต๋ชจ์„ธํฌ์ข…์˜ ๋‘ ๊ฐ€์ง€ ํ•˜์œ„ ์œ ํ˜•, ์ฆ‰ ์—ผ์ƒ‰์ฒด 1p์™ฟ’ 19q์˜ ์†Œ์‹ค๋กœ ํŠน์ง•์ง€์–ด์ง€๋Š” Aํ˜•๊ณผ TP53 ๋ฐ ATRX ๋Œ์—ฐ๋ณ€์ด๋กœ ํŠน์ง•์ง€์–ด์ง€๋Š” Bํ˜• ๊ฐ„์˜ ์ƒ์กด ์ฐจ์ด๋ฅผ ํ™•์ธํ•˜์˜€๋‹ค. Kaplan-Meier ๋ถ„์„ ๊ฒฐ๊ณผ, Aํ˜• ๊ทธ๋ฃน์ด Bํ˜• ๊ทธ๋ฃน์— ๋น„ํ•ด ์œ ์˜๋ฏธํ•˜๊ฒŒ ๋†’์€ ์ƒ์กด์œจ์„ ๋ณด์˜€๋‹ค. ์ด๋Š” TP53๊ณผ ATRX ์œ ์ „์ž์˜ ๊ธฐ๋Šฅ ์†์‹ค์ด ์•” ๋ฐœ์ƒ๊ณผ ์ง„ํ–‰์— ์ค‘์š”ํ•œ ์—ญํ• ์„ ํ•œ๋‹ค๋Š” ๊ฒƒ์„ ๋ณด์—ฌ์ค€๋‹ค. ๋˜ํ•œ ์ด ์‹คํ—˜์€ Xena ๋ธŒ๋ผ์šฐ์ €๋ฅผ ํ™œ์šฉํ•˜์—ฌ ๋‹ค์–‘ํ•œ ์œ ์ „์ฒด ๋ฐ์ดํ„ฐ๋ฅผ ํ†ตํ•ฉ์ ์œผ๋กœ ๋ถ„์„ํ•  ์ˆ˜ ์žˆ์Œ์„ ์‹œ์‚ฌํ•œ๋‹ค. ๊ฒฐ๊ณผ์ ์œผ๋กœ ์ด ๋ฌธ์„œ๋Š” ์•” ์œ ์ „์ฒดํ•™ ์—ฐ๊ตฌ์— ์žˆ์–ด Xena ๋ธŒ๋ผ์šฐ์ €์˜ ํ™œ์šฉ ๊ฐ€์น˜์™ฟ’ ์ค‘์š”์„ฑ์„ ์ž˜ ๋ณด์—ฌ์ฃผ๊ณ  ์žˆ๋‹ค.
  • ์ž๋ฃŒํ›„๊ธฐ

      Ai ๋ฆฌ๋ทฐ
      UCSC Xena ๋ธŒ๋ผ์šฐ์ €๋ฅผ ์ด์šฉํ•œ ์•” ์œ ์ „์ฒด ๋ฐ์ดํ„ฐ ์‹œ๊ฐํ™” ๋ฐ ๋ถ„์„์— ๋Œ€ํ•œ ์ƒ์„ธํ•œ ์‹คํ—˜ ๊ฒฐ๊ณผ๋ฅผ ์ œ๊ณตํ•˜๊ณ  ์žˆ์œผ๋ฉฐ, ๋‚ฎ์€ ๋“ฑ๊ธ‰ ๊ต๋ชจ์„ธํฌ์ข…์˜ ๋‘ ๊ฐ€์ง€ ํ•˜์œ„ ์œ ํ˜• ๊ฐ„ ์ƒ์กด ์ฐจ์ด๋ฅผ Kaplan-Meier ๋ถ„์„์„ ํ†ตํ•ด ํ™•์ธํ•˜์˜€๋‹ค.
    • ์ž์ฃผ๋ฌป๋Š”์งˆ๋ๅฉ์˜ ๋‹ต๋ณ€์„ ํ™•์ธํ•ด ์ฃผ์„ธ์š”

      ํ•ดํ”ผ์บ ํผ์Šค FAQ ๋”๋ต–๊ธฐ

      ๊ผญ ์•Œ์•„์ฃผ์„ธ์š”

      • ์ž๋ฃŒ์˜ ์ •๋ณด ๋ฐ ๋‚ด์šฉ์˜ ์ง„์‹ค์„ฑ์— ๋Œ€ํ•˜์—ฌ ํ•ดํ”ผ์บ ํผ์Šค๋Š” ๋ณด์ฆํ•˜์ง€ ์•Š์œผ๋ฉฐ, ํ•ด๋‹น ์ •๋ณด ๋ฐ ๊ฒŒ์‹œ๋ฌผ ์ €์ž‘๊ถŒ๊ณผ ๊ธฐํƒ€ ๋ฒ•์  ์ฑ…์ž„์€ ์ž๋ฃŒ ๋“ฑ๋ก์ž์—๊ฒŒ ์žˆ์Šต๋‹ˆ๋‹ค.
        ์ž๋ฃŒ ๋ฐ ๊ฒŒ์‹œ๋ฌผ ๋‚ด์šฉ์˜ ๋ถˆ๋ฒ•์  ์ด์šฉ, ๋ฌด๋‹จ ์ „์žฌโˆ™๋ฐฐํฌ๋Š” ๊ธˆ์ง€๋˜์–ด ์žˆ์Šต๋‹ˆ๋‹ค.
        ์ €์ž‘๊ถŒ์นจํ•ด, ๋ช…์˜ˆํ›ผ์† ๋“ฑ ๋ถ„์Ÿ ์š”์†Œ ๋ฐœ๊ฒฌ ์‹œ ๊ณ ๊ฐ๋น„๋ฐ”์นด์ง€๋…ธ Viva์˜ ์ €์ž‘๊ถŒ์นจํ•ด ์‹ ๊ณ ๋น„๋ฐ”์นด์ง€๋…ธ Viva๋ฅผ ์ด์šฉํ•ด ์ฃผ์‹œ๊ธฐ ๋ฐ”๋ž๋‹ˆ๋‹ค.
      • ํ•ดํ”ผ์บ ํผ์Šค๋Š” ๊ตฌ๋งค์ž์™ฟ’ ํŒ๋งค์ž ๋ชจ๋‘๊ฐ€ ๋งŒ์กฑํ•˜๋Š” ์„œ๋น„์Šค๊ฐ€ ๋˜๋„๋ก ๋…ธ๋ ฅํ•˜๊ณ  ์žˆ์œผ๋ฉฐ, ์•„๋ž˜์˜ 4๊ฐ€์ง€ ์ž๋ฃŒํ™˜๋ถˆ ์กฐ๊ฑด์„ ๊ผญ ํ™•์ธํ•ด์ฃผ์‹œ๊ธฐ ๋ฐ”๋ž๋‹ˆ๋‹ค.
        ํŒŒ์ผ์˜ค๋ฅ˜ ์ค‘๋ณต์ž๋ฃŒ ์ €์ž‘๊ถŒ ์—†์Œ ์„ค๋ช…๊ณผ ์‹ค์ œ ๋‚ด์šฉ ๋ถˆ์ผ์น˜
        ํŒŒ์ผ์˜ ๋‹ค์šด๋กœ๋“œ๊ฐ€ ์ œ๋Œ€๋กœ ๋˜์ง€ ์•Š๊ฑฐ๋‚˜ ํŒŒ์ผํ˜•์‹์— ๋งž๋Š” ํ”„๋กœ๊ทธ๋žจ์œผ๋กœ ์ •์ƒ ์ž‘๋™ํ•˜์ง€ ์•Š๋Š” ๊ฒฝ์šฐ ๋‹ค๋ฅธ ์ž๋ฃŒ์™ฟ’ 70% ์ด์ƒ ๋‚ด์šฉ์ด ์ผ์น˜ํ•˜๋Š” ๊ฒฝ์šฐ (์ค‘๋ณต์ž„์„ ํ™•์ธํ•  ์ˆ˜ ์žˆ๋Š” ๊ทผ๊ฑฐ ํ•„์š”ํ•จ) ์ธํ„ฐ๋„ท์˜ ๋‹ค๋ฅธ ์‚ฌ์ดํŠธ, ์—ฐ๊ตฌ๊ธฐ๊ด€, ํ•™๊ป“, ์„œ์  ๋“ฑ์˜ ์ž๋ฃŒ๋ฅผ ๋„์šฉํ•œ ๊ฒฝ์šฐ ์ž๋ฃŒ์˜ ์„ค๋ช…๊ณผ ์‹ค์ œ ์ž๋ฃŒ์˜ ๋‚ด์šฉ์ด ์ผ์น˜ํ•˜์ง€ ์•Š๋Š” ๊ฒฝ์šฐ
    ๋ฌธ์„œ ์ดˆ์•ˆ์„ ์ƒ์„ฑํ•ด์ฃผ๋Š” EasyAI
    ์•ˆ๋…•ํ•˜์„ธ์š”. ํ•ดํ”ผ์บ ํผ์Šค์˜ ๋ฐฉ๋Œ€ํ•œ ์ž๋ฃŒ ์ค‘์—์„œ ์„ ๋ณ„ํ•˜์—ฌ ๋‹น์‹ ๋งŒ์˜ ์ดˆ์•ˆ์„ ๋งŒ๋“ค์–ด์ฃผ๋Š” EasyAI ์ž…๋‹ˆ๋‹ค.
    ์ €๋Š” ์•„๋ž˜์™ฟ’ ๊ฐ™์ด ์ž‘์—…์„ ๋„์™ฟ’๋“œ๋ฆฝ๋‹ˆ๋‹ค.
    - ์ฃผ์ œ๋งŒ ์ž…๋ ฅํ•˜๋ฉด ๋ชฉ์ฐจ๋ถ€ํ„ฐ ๋ณธ๋ๅฉ๋‚ด์šฉ๊นŒ์ง€ ์ž๋™ ์ƒ์„ฑํ•ด ๋“œ๋ฆฝ๋‹ˆ๋‹ค.
    - ์žฅ๋ฌธ์˜ ์ฝ˜ํ…์ธ ๋ฅผ ์‰ฝ๊ณ  ๋น ๋ฅด๊ฒŒ ์ž‘์„ฑํ•ด ๋“œ๋ฆฝ๋‹ˆ๋‹ค.
    - ์Šคํ† ์–ด์—์„œ ๋ฌด๋ฃŒ ์บ์‹œ๋ฅผ ๊ณ„์ •๋ณ„๋กœ 1ํšŒ ๋ฐœ๊ธ‰ ๋ฐ›์„ ์ˆ˜ ์žˆ์Šต๋‹ˆ๋‹ค. ์ง€๊ธˆ ๋ฐ”๋กœ ์ฒดํ—˜ํ•ด ๋ณด์„ธ์š”!
    ์ด๋Ÿฐ ์ฃผ์ œ๋“ค์„ ์ž…๋ ฅํ•ด ๋ณด์„ธ์š”.
    - ์œ ์•„์—๊ฒŒ ์ ํ•ฉํ•œ ๋ฌธํ•™์ž‘ํ’ˆ์˜ ๊ธฐ์ค€๊ณผ ํŠน์„ฑ
    - ํ•œ๊ตญ์ธ์˜ ๊ฐ€์น˜๊ด€ ์ค‘์—์„œ ์ •์‹ ์  ๊ฐ€์น˜๊ด€์„ ์ด๋ฃจ๋Š” ๊ฒƒ๋“ค์„ ๋ฌธํ™”์  ๋ฌธ๋ฒ•์œผ๋กœ ์ •๋ฆฌํ•˜๊ณ , ํ˜„๋Œ€ํ•œ๊ตญ์‚ฌํšŒ์—์„œ ์ผ์–ด๋‚˜๋Š” ์‚ฌ๊ฑด๊ณผ ์‚ฌ๊ณ ๋ฅผ ๋น„๊ตํ•˜์—ฌ ์ž์‹ ์˜ ์˜๊ฒฌ์œผ๋กœ ๊ธฐ์ˆ ํ•˜์„ธ์š”
    - ์ž‘๋ณ„์ธ์‚ฌ ๋…ํ›„๊ฐ
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    ์ฑ—๋ด‡์œผ๋กœ ๊ฐ„ํŽธํ•˜๊ฒŒ ์ƒ๋‹ดํ•ด๋ณด์„ธ์š”.
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