Karyotype and DNA-Methylation Responses in Myelodysplastic Syndromes following Treatment with Traditional Chinese Formula Containing Arsenic

Table 4

Functions of genes with hypermethylation after treatment.

Go_id	Go_name	Diffgene; _count	𝑃 value	FDR
GO:0007596	Blood coagulation	13	2.09𝐸−04	2.11𝐸−02
GO:0007088	regulation of mitosis	3	2.36𝐸−04	2.11𝐸−02
GO:0016337	Cell-cell adhesion	5	5.61𝐸−04	2.55𝐸−02
GO:0006357	Regulation of transcription from; RNA polymerase II promoter	8	5.72𝐸−04	2.56𝐸−02
GO:0006325	Chromatin organization	3	1.11𝐸−03	3.05𝐸−02
GO:0006890	Retrograde vesicle-mediated transport,; Golgi to ER	3	1.54𝐸−03	3.22𝐸−02
GO:0032312	Regulation of ARF GTPase activity	2	1.64𝐸−03	3.25𝐸−02
GO:0033690	Positive regulation of osteoblast proliferation	2	2.44𝐸−03	3.79𝐸−02
GO:0060710	Chorioallantoic fusion	2	2.44𝐸−03	3.79𝐸−02
GO:0006364	rRNA processing	4	3.02𝐸−03	4.05𝐸−02
GO:0043069	Negative regulation of programmed cell death	2	3.39𝐸−03	4.19𝐸−02
GO:0015031	Protein transport	9	3.50𝐸−03	4.22𝐸−02
GO:0005975	Carbohydrate metabolic process	8	4.92𝐸−03	4.56𝐸−02
GO:0006355	Regulation of transcription, DNA-dependent	20	5.43𝐸−03	4.65𝐸−02
GO:0007155	Cell adhesion	11	5.45𝐸−03	4.66𝐸−02
GO:0042953	Lipoprotein transport	2	5.75𝐸−03	4.70𝐸−02
GO:0048863	Stem cell differentiation	2	5.75𝐸−03	4.70𝐸−02
GO:0009395	Phospholipid catabolic process	2	7.14𝐸−03	4.87𝐸−02

This table shows functions of genes with hypermethylation after treatment. go_id: gene ID number in Gene Ontology database; go_name: category of function of gene; diffgene_count: number of gene methylated; 𝑃 value: 𝑃<0.01 indicating methylation is significant; FDR: false discovery rate, 𝑃<0.05 as filter cutoff rate.