SBM Lab
시스템 생물학 & 바이오인포매틱스 블로그. 프로테오믹스, 바이오마커, 건강과학에 대한 연구 기반 콘텐츠를 제공합니다.
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2~4개 세트를 비교하고 PNG/SVG로 다운로드하세요. 유전자 비교, DEG overlap, 데이터 분석에 활용 가능합니다.
바로 사용하기최신 글
WGCNA는 정말 효과가 있을까 — 공개 단백체 데이터로 처음부터 끝까지 재 본 결과
CPTAC 신장암 종양 110개로 WGCNA 표준 흐름을 돌리고 다른 코호트에서 다시 확인했습니다. 모듈은 진짜였지만, 등급과 유의한 모듈 7개 중 같은 크기 무작위 묶음을 넘은 것은 2개였고 가장 센 모듈은 혈관 함량이었습니다.
Does WGCNA Really Work? Running It End to End on Public Proteomics Data
We ran the standard WGCNA flow on 110 CPTAC kidney tumours and re-checked it in a second cohort. Modules are real, but only 2 of 7 grade-linked modules beat size-matched random sets, and the top one was blood-vessel content.
STRING Confidence Score and Hub Proteins, Measured: What 0.4 vs 0.7 Changes and Whether Hubs Are Biology or Attention (STRING 12.5)
Measured on STRING 12.5: 37% of links at the default 0.4 cut-off need text mining, the top hub at 0.4 has 17 papers, and random protein lists look significantly connected 20/20 times.
더 보기
DIA-NN Quantification Modes Scored on Known Ratios: QuantUMS, Legacy MaxLFQ and Fragment-Level Re-Quantification, With and Without MBR
One set of DIA-NN 2.3.2 identifications, seven ways to turn it into protein quantities, scored against known ratios. Without MBR the MaxLFQ-type routes land within about 4 points of each other. With MBR, the strongly changed proteins MBR adds are compressed: QuantUMS handles them best, and re-quantifying them from raw fragments is much worse.
Proteomics CV: What Replicate CVs Look Like in MaxQuant, FragPipe and DIA-NN (Measured on a Known-Ratio Benchmark)
Median replicate CV on the same public benchmark: DIA-NN 4.5%, MaxQuant LFQ 8.1%, FragPipe 10.1%, and 20.9% for MaxQuant's raw Intensity column. Why the number depends on the column, on which proteins survive, and on abundance, and whether a low CV means a correct ratio.
Best Bioinformatics Tools in 2026, Installed and Timed: What I Actually Ran This Month
Not a list of names: the proteomics, RNA-seq and single-cell tools I installed and ran on public data in October 2026, with versions, run times, the install traps I hit, and licences.
Proteomics vs Genomics: How Much Does mRNA Tell You About Protein? Measured in 29 Human Tissues
The practical difference between genomics and proteomics, measured: in paired mRNA and protein data from 29 healthy human tissues, mRNA explained about 29% of the variation in protein levels, and a gene's mRNA and protein tracked each other across tissues only weakly (median Spearman 0.35).
Biomarker Discovery and Data Leakage: Shuffled Labels Still Scored AUC 0.75 on a Real CSF Proteome
On a public CSF proteomics cohort, I shuffled the disease labels so no real signal remained. Picking proteins before cross-validation still gave a mean AUC of 0.73 (up to 0.84), and up to 0.88 on 'external' cohorts. Doing it properly gave 0.5.
DIA-NN 2.3 on a Known-Answer Benchmark: How It Compares With MaxQuant and FragPipe (and Why the Comparison Has a Catch)
DIA-NN 2.3.2 on public SWATH runs with known ratios, scored like my MaxQuant and FragPipe runs: most proteins, tightest ratios, but a different instrument. Commands, timings and traps.