RPKM/FPKM. 主要适用于：组内样本内比较. 不适用于：组间样本间比较（差异分析）、组内重复样本间比较. 主要考虑的是：测序深度和基因长度. Reference: rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/ StatQuest学习笔记24——RPKM FPKM TPM

FPKM Description. Fragments Per Kilobase of transcript per Million mapped reads (FPKM) is a simple expression level normalization method. The FPKM normalizes read count based on gene length and the total number of mapped reads. Overview. FPKM is implemented at the GDC on gene-level read counts that are produced by STAR 1 and generated using ...

2024年11月23日 · 全称为 Fragments Per Kilobase of exon model per Million mapped fragments ，FPKM与RPKM的原理类似，区别在于FPKM是Fragments，而RPKM则是reads。 在二代RNA-Seq建库时把DNA打断成小片段（fragment）后加上接头，然后再测序。

2021年6月22日 · We compared the reproducibility across replicate samples based on TPM (transcripts per million), FPKM (fragments per kilobase of transcript per million fragments mapped), and normalized counts using coefficient of variation, intraclass correlation coefficient, and cluster analysis.

2021年4月10日 · Pyruvate kinase M2 (PKM2), a key rate-limiting enzyme of glycolysis, is a critical regulator in tumor metabolism. PKM2 has been demonstrated to overexpressed in various cancers and promoted proliferation and metastasis of tumor cells. The errant expression of PKM2 has inspired people to investigate …

2021年4月10日 · Pyruvate kinase M2 (PKM2), a key rate-limiting enzyme of glycolysis, is a critical regulator in tumor metabolism. PKM2 has been demonstrated to overexpressed in various cancers and promoted proliferation and metastasis of tumor cells.

2020年3月1日 · Several studies demonstrated that the expression of PKM2 is up-regulated in colorectal cancer patients (CRC) and inflammatory bowel disease and intrahepatic cholangiocarcinoma (ICC) tissues with high tumor cell necrosis, high angiogenesis, and more advanced stages.

2024年2月8日 · In this review, we first introduce the role of PKM2 in various biological processes of tumor growth. Then, we summarize the aggregation regulation mechanism of PKM2 by various endogenous cofactors such as Fructose-1, 6-diphosphate (FBP), various amino acids, and post-translational modification (PTMs).

RNA-Seq expression level read counts produced by the workflow are normalized using three commonly used methods: FPKM, FPKM-UQ, and TPM. Normalized values should be used only within the context of the entire gene set. Users are encouraged to normalize raw read count values if a subset of genes is investigated.

To this end, normal human fibroblasts were genetically-engineered to express the two isoforms of pyruvate kinase M (PKM1 and PKM2), a key enzyme in the glycolytic pathway. In a xenograft model, fibroblasts expressing PKM1 or PKM2 greatly promoted the growth of co-injected MDA-MB-231 breast cancer cells, without an increase in tumor angiogenesis.