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Table 1 Top regulated proteins: integrate analysis of three-omics

From: Revealing the pathogenic changes of PAH based on multiomics characteristics

Correlation Methylation information
Gene symbol mRNA_ID Protein full name FC dir p FDR Chr Info1 Info2 Info3
S100a9 ENSRNOT00000015351 Protein S100-A9 5.8 Up 1.2E−04 1.9E−02 chr2 Intron First intron NA
Ttc29 ENSRNOT00000089569 Tetratricopeptide repeat protein 29 0.3 Down 7.9E−05 8.8E−03 chr19 Exon Internal exon NA
Bicc1 MSTRG.12240.6 BicC family RNA-binding protein 1 5.2 Up 5.0E−04 4.5E−02 chr20 Intron Internal intron NA
Tnc ENSRNOT00000084563 Tenascin C 0.0 Down 7.1E−07 1.6E−04 chr5 Intron Internal intron NA
Runx1 MSTRG.4485.1 Runt-related transcription factor 1 0.6 Down 5.4E−05 8.5E−03 chr11 Intron First intron NA
Picalm ENSRNOT00000092945 Clathrin-assembly lymphoid myeloid leukemia protein 8.7 Up 2.1E−13 1.4E−10 chr1 Intron Internal intron NA
Cdyl2 ENSRNOT00000068440 Chromodomain Y-like 2 0.3 Down 1.4E−04 1.4E−02 chr19 Intron Internal intron NA
Gfpt2 ENSRNOT00000003770 Glutamine-fructose-6-phosphate aminotransferase 2 0.8 Down 3.9E−05 5.1E−03 chr10 Intron Internal intron NA
Folr2 MSTRG.1446.1 Folate receptor 2 0.2 Down 8.7E−05 1.2E−02 chr1 Promoter Distal LCP
Slc43a2 MSTRG.3515.3 Solute carrier family 43 member 2 17.7 Up 2.2E−19 3.0E−16 chr10 Intron Internal intron NA
Myh6 ENSRNOT00000023302 Myosin-6 2.8 Up 4.8E−05 8.6E−03 chr15 Intron Internal intron NA
RGD1563354 ENSRNOT00000019453 Similar to hypothetical protein D630003M21 0.2 Down 5.6E−06 1.1E−03 chr3 Promoter Distal LCP
Hist2h2ac ENSRNOT00000051917 Histone H2A 0.2 down 9.0E−08 3.0E−05 chr2 Promoter Intermediate ICP
Map4k2 ENSRNOT00000064798 Mitogen-activated protein kinase 4.9 up 3.4E−06 6.8E−04 chr1 Intron Internal intron NA
Gsta3 ENSRNOT00000088416 Glutathione S-transferase alpha-3 2.7 up 2.3E−04 9.2E−06 chr9 Exon Last exon NA
Pdk4 ENSRNOT00000012760 Pyruvate dehydrogenase kinase, isoenzyme 4 0.2 down 7.9E−09 2.7E−06 chr4 Promoter Proximal LCP
Med12 l ENSRNOT00000084020 Mediator complex subunit 12-like 6.5 Up 1.3E−08 5.0E−06 chr2 Promoter Distal LCP
Mapk10 ENSRNOT00000065965 Mitogen-activated protein kinase 2.6 Up 3.6E−06 8.0E−04 chr14 Intron First intron NA
Cd63 ENSRNOT00000090381 Ad1-antigen 0.5 Down 3.6E−06 7.0E−04 chr7 Promoter Intermediate ICP
Krt1 ENSRNOT00000034450 Keratin, type II cytoskeletal 1 21.8 Up 3.6E−04 3.9E−02 chr7 Promoter Distal LCP
Correlation mRNA information Protein information
Gene symbol mRNA_ID Protein full name FC dir p FDR FC dir p FDR
S100a9 ENSRNOT00000015351 Protein S100-A9 2.4 Up 0.05 0.82 1.6 Up 6.6E−11 4.5E−10
Ttc29 ENSRNOT00000089569 Tetratricopeptide repeat protein 29 1.0 Down 0.22 0.84 1.5 Up 1.9E−10 1.2E−09
Bicc1 MSTRG.12240.6 BicC family RNA-binding protein 1 0.8 Down 0.38 0.84 1.5 Up 1.2E−05 2.8E−05
Tnc ENSRNOT00000084563 Tenascin C 2.2 Up 0.36 0.84 1.5 Up 1.5E−12 1.5E−11
Runx1 MSTRG.4485.1 Runt-related transcription factor 1 1.5 Up 0.3 0.84 1.5 Up 3.2E−10 1.9E−09
Picalm ENSRNOT00000092945 Clathrin-assembly lymphoid myeloid leukemia protein 0.6 Down 0.04 0.82 1.5 Up 1.6E−10 1.0E−09
Cdyl2 ENSRNOT00000068440 Chromodomain Y-like 2 1.1 Up 0.24 0.84 1.4 Up 9.9E−16 2.7E−14
Gfpt2 ENSRNOT00000003770 Glutamine-fructose-6-phosphate aminotransferase 2 1.5 Up 0.1 0.82 1.4 Up 1.7E−17 9.4E−16
Folr2 MSTRG.1446.1 Folate receptor 2 1.4 Up 0.15 0.84 1.4 Up 6.4E−18 4.3E−16
Slc43a2 MSTRG.3515.3 Solute carrier family 43 member 2 1.7 Up 0.35 0.84 1.4 Up 5.1E−08 1.9E−07
Myh6 ENSRNOT00000023302 Myosin-6 1.0 Down 0.31 0.84 0.7 Down 6.8E−16 2.0E−14
RGD1563354 ENSRNOT00000019453 Similar to hypothetical protein D630003M21 1.7 Up 0.06 0.82 0.7 Down 1.6E−11 1.2E−10
Hist2h2ac ENSRNOT00000051917 Histone H2A 1.1 Up 0.51 0.84 0.7 Down 8.6E−07 2.6E−06
Map4k2 ENSRNOT00000064798 Mitogen-activated protein kinase 1.3 Up 0.08 0.82 0.6 Down 2.4E−14 4.2E−13
Gsta3 ENSRNOT00000088416 Glutathione S-transferase alpha-3 0.8 Down 0.31 0.84 0.6 Down 2.9E−15 6.6E−14
Pdk4 ENSRNOT00000012760 Pyruvate dehydrogenase kinase, isoenzyme 4 0.3 Down 0.05 0.82 0.6 Down 5.5E−19 5.8E−17
Med12 l ENSRNOT00000084020 Mediator complex subunit 12-like 1.0 Down 0.02 0.82 0.6 Down 2.2E−04 4.4E−04
Mapk10 ENSRNOT00000065965 Mitogen-activated protein kinase 1.0 Down 0.41 0.84 0.6 Down 6.7E−04 1.2E−03
Cd63 ENSRNOT00000090381 Ad1-antigen 1.3 Up 0.47 0.84 0.6 Down 4.8E−03 7.7E−03
Krt1 ENSRNOT00000034450 Keratin, type II cytoskeletal 1 0.7 Down 0.02 0.82 0.4 Down 4.2E−17 1.9E−15
  1. Top 10 upregulated and downregulated proteins identified among the three omics analyses. These three omics are correlated in the table, including methylation information, mRNA information and protein information. The fold change (FC), the direction (dir), p value (p) and FDR of three omics information are shown. Meanwhile, the chromosomal localization (Chr) and methylated positions (Info1–3) are also shown. Info1–3 shows the concrete methylated locations