TCGA数据库里面的乳腺癌样本RNA-seq数据配对的

灵感来自于 2008和2009年 Venables 做的工作,用传统的RT-PCR 来分析可变剪切

Recently, Venables et al. used RT-PCR to screen 600 cancer-associated genes [18] and 2168 alternatively spliced exons (ASEs) [19] in human breast tumors versus normal breast tissues.

TCGA数据库的原始fastq数据并不好下载,但是下载之后可以做很多事情,比如这篇2015年的文章:Genome-wide analysis of alternative transcripts in human breast cancer 作者,Raw RNA-Seq reads of breast cancer and matched normal tissues of 105 patients were obtained from the TCGA database [20]. TCGA sample IDs for the patients and RNA-Seq information are listed in File S1.

结论

We identified 2839 genes, ~10 % of protein-coding genes in the human genome, that had differential expression of transcript variants between tumors and healthy tissues. The validity of the computational analysis was confirmed by quantitative RT-PCR assessment of transcript variant expression from four top candidate genes. The alternative transcript profiling led to classification of breast cancer into two subgroups and yielded a novel molecular signature that could be prognostic of patients’ tumor burden and survival. We uncovered nine splicing factors (FOX2, MBNL1, QKI, PTBP1, ELAVL1, HNRNPC, KHDRBS1, SFRS2, and TIAR) that were involved in aberrant splicing in breast cancer. Network analyses for the coordinative patterns of transcript variant expression identified twelve “hub” genes that differentiated the cancerous and normal transcriptomes.

样本如下表:

Patient ID TCGA sample barcode cell type # of reads # of aligned reads
TCGA-A7-A0D9 TCGA-A7-A0D9-01A-31R-A056-07 tumor 138,808,376 126,188,164
TCGA-A7-A0D9 TCGA-A7-A0D9-11A-53R-A089-07 normal 131,937,994 121,138,444
TCGA-A7-A0DB TCGA-A7-A0DB-01A-11R-A00Z-07 tumor 156,166,804 138,950,207
TCGA-A7-A0DB TCGA-A7-A0DB-11A-33R-A089-07 normal 118,421,444 107,977,929
TCGA-A7-A0DC TCGA-A7-A0DC-01A-11R-A00Z-07 tumor 172,265,062 158,627,891
TCGA-A7-A0DC TCGA-A7-A0DC-11A-41R-A089-07 normal 123,750,188 112,217,508
TCGA-A7-A13G TCGA-A7-A13G-01A-11R-A13Q-07 tumor 191,223,166 178,368,911
TCGA-A7-A13G TCGA-A7-A13G-11A-51R-A13Q-07 normal 182,456,432 166,379,451
TCGA-AC-A23H TCGA-AC-A23H-01A-11R-A157-07 tumor 177,033,742 162,674,793
TCGA-AC-A23H TCGA-AC-A23H-11A-12R-A157-07 normal 178,308,422 164,165,269
TCGA-AC-A2FB TCGA-AC-A2FB-01A-11R-A17B-07 tumor 169,676,200 156,614,211
TCGA-AC-A2FB TCGA-AC-A2FB-11A-13R-A17B-07 normal 190,190,692 174,099,327
TCGA-AC-A2FF TCGA-AC-A2FF-01A-11R-A17B-07 tumor 174,009,858 159,949,817
TCGA-AC-A2FF TCGA-AC-A2FF-11A-13R-A17B-07 normal 194,470,230 179,374,034
TCGA-BH-A0AY TCGA-BH-A0AY-01A-21R-A00Z-07 tumor 137,979,390 120,775,450
TCGA-BH-A0AY TCGA-BH-A0AY-11A-23R-A089-07 normal 127,264,540 112,686,808
TCGA-BH-A0AZ TCGA-BH-A0AZ-01A-21R-A12P-07 tumor 121,847,260 114,379,483
TCGA-BH-A0AZ TCGA-BH-A0AZ-11A-22R-A12P-07 normal 169,117,198 158,131,428
TCGA-BH-A0B2 TCGA-BH-A0B2-01A-11R-A10J-07 tumor 132,164,936 122,727,577
TCGA-BH-A0B2 TCGA-BH-A0B2-11A-11R-A10J-07 normal 136,217,762 123,411,270
TCGA-BH-A0B3 TCGA-BH-A0B3-01A-11R-A056-07 tumor 151,127,170 141,937,642
TCGA-BH-A0B3 TCGA-BH-A0B3-11B-21R-A089-07 normal 150,169,986 140,192,817
TCGA-BH-A0B5 TCGA-BH-A0B5-01A-11R-A12P-07 tumor 146,366,446 140,779,538
TCGA-BH-A0B5 TCGA-BH-A0B5-11A-23R-A12P-07 normal 155,514,650 148,928,956
TCGA-BH-A0B7 TCGA-BH-A0B7-01A-12R-A115-07 tumor 144,909,574 139,431,251
TCGA-BH-A0B7 TCGA-BH-A0B7-11A-34R-A115-07 normal 123,455,904 115,065,775
TCGA-BH-A0B8 TCGA-BH-A0B8-01A-21R-A056-07 tumor 118,140,974 111,947,104
TCGA-BH-A0B8 TCGA-BH-A0B8-11A-41R-A089-07 normal 141,727,898 131,043,696
TCGA-BH-A0BC TCGA-BH-A0BC-01A-22R-A084-07 tumor 176,105,252 164,929,394
TCGA-BH-A0BC TCGA-BH-A0BC-11A-22R-A089-07 normal 124,633,294 115,759,870
TCGA-BH-A0BJ TCGA-BH-A0BJ-01A-11R-A056-07 tumor 138,525,486 132,161,133
TCGA-BH-A0BJ TCGA-BH-A0BJ-11A-23R-A089-07 normal 126,785,800 118,395,744
TCGA-BH-A0BM TCGA-BH-A0BM-01A-11R-A056-07 tumor 108,081,728 89,823,378
TCGA-BH-A0BM TCGA-BH-A0BM-11A-12R-A089-07 normal 134,757,364 123,370,502
TCGA-BH-A0BQ TCGA-BH-A0BQ-01A-21R-A115-07 tumor 112,152,776 107,892,894
TCGA-BH-A0BQ TCGA-BH-A0BQ-11A-33R-A115-07 normal 124,573,688 117,447,905
TCGA-BH-A0BS TCGA-BH-A0BS-01A-11R-A12P-07 tumor 152,727,224 146,319,635
TCGA-BH-A0BS TCGA-BH-A0BS-11A-11R-A12P-07 normal 150,072,852 142,030,386
TCGA-BH-A0BT TCGA-BH-A0BT-01A-11R-A12P-07 tumor 141,382,620 134,189,783
TCGA-BH-A0BT TCGA-BH-A0BT-11A-21R-A12P-07 normal 128,109,708 122,178,984
TCGA-BH-A0BV TCGA-BH-A0BV-01A-11R-A00Z-07 tumor 129,166,776 123,327,266
TCGA-BH-A0BV TCGA-BH-A0BV-11A-31R-A089-07 normal 174,140,560 163,729,694
TCGA-BH-A0BW TCGA-BH-A0BW-01A-11R-A115-07 tumor 136,368,260 126,958,557
TCGA-BH-A0BW TCGA-BH-A0BW-11A-12R-A115-07 normal 132,150,766 122,361,468
TCGA-BH-A0C0 TCGA-BH-A0C0-01A-21R-A056-07 tumor 115,541,510 107,476,181
TCGA-BH-A0C0 TCGA-BH-A0C0-11A-21R-A089-07 normal 171,649,006 160,546,023
TCGA-BH-A0C3 TCGA-BH-A0C3-01A-21R-A12P-07 tumor 124,165,018 118,212,892
TCGA-BH-A0C3 TCGA-BH-A0C3-11A-23R-A12P-07 normal 140,232,116 134,046,435
TCGA-BH-A0DD TCGA-BH-A0DD-01A-31R-A12P-07 tumor 139,181,120 132,072,091
TCGA-BH-A0DD TCGA-BH-A0DD-11A-23R-A12P-07 normal 143,825,590 138,764,921
TCGA-BH-A0DG TCGA-BH-A0DG-01A-21R-A12P-07 tumor 130,991,102 125,187,910
TCGA-BH-A0DG TCGA-BH-A0DG-11A-43R-A12P-07 normal 161,690,464 153,973,399
TCGA-BH-A0DH TCGA-BH-A0DH-01A-11R-A084-07 tumor 141,347,808 133,373,467
TCGA-BH-A0DH TCGA-BH-A0DH-11A-31R-A089-07 normal 148,277,572 139,085,476
TCGA-BH-A0DK TCGA-BH-A0DK-01A-21R-A056-07 tumor 132,755,722 124,736,397
TCGA-BH-A0DK TCGA-BH-A0DK-11A-13R-A089-07 normal 177,010,816 168,266,065
TCGA-BH-A0DO TCGA-BH-A0DO-01B-11R-A12D-07 tumor 143,358,002 137,382,140
TCGA-BH-A0DO TCGA-BH-A0DO-11A-22R-A12D-07 normal 142,919,934 136,428,939
TCGA-BH-A0DP TCGA-BH-A0DP-01A-21R-A056-07 tumor 124,918,206 117,156,705
TCGA-BH-A0DP TCGA-BH-A0DP-11A-12R-A089-07 normal 155,978,948 144,763,543
TCGA-BH-A0DQ TCGA-BH-A0DQ-01A-11R-A084-07 tumor 133,272,538 124,963,346
TCGA-BH-A0DQ TCGA-BH-A0DQ-11A-12R-A089-07 normal 185,461,378 174,223,263
TCGA-BH-A0DT TCGA-BH-A0DT-01A-21R-A12D-07 tumor 129,537,134 124,262,182
TCGA-BH-A0DT TCGA-BH-A0DT-11A-12R-A12D-07 normal 139,790,298 133,785,140
TCGA-BH-A0DV TCGA-BH-A0DV-01A-21R-A12P-07 tumor 183,452,856 177,301,378
TCGA-BH-A0DV TCGA-BH-A0DV-11A-22R-A12P-07 normal 158,251,822 150,308,324
TCGA-BH-A0E0 TCGA-BH-A0E0-01A-11R-A056-07 tumor 101,563,412 94,471,287
TCGA-BH-A0E0 TCGA-BH-A0E0-11A-13R-A089-07 normal 131,963,864 121,217,378
TCGA-BH-A0E1 TCGA-BH-A0E1-01A-11R-A056-07 tumor 129,133,298 122,877,196
TCGA-BH-A0E1 TCGA-BH-A0E1-11A-13R-A089-07 normal 114,415,344 106,471,967
TCGA-BH-A0H7 TCGA-BH-A0H7-01A-13R-A056-07 tumor 175,916,242 168,215,671
TCGA-BH-A0H7 TCGA-BH-A0H7-11A-13R-A089-07 normal 140,699,278 131,018,817
TCGA-BH-A0HA TCGA-BH-A0HA-01A-11R-A12P-07 tumor 125,599,414 118,368,658
TCGA-BH-A0HA TCGA-BH-A0HA-11A-31R-A12P-07 normal 134,567,754 127,687,489
TCGA-BH-A0HK TCGA-BH-A0HK-01A-11R-A056-07 tumor 125,630,164 119,084,112
TCGA-BH-A0HK TCGA-BH-A0HK-11A-11R-A089-07 normal 149,845,140 134,227,874
TCGA-BH-A18J TCGA-BH-A18J-01A-11R-A12D-07 tumor 152,769,144 147,051,181
TCGA-BH-A18J TCGA-BH-A18J-11A-31R-A12D-07 normal 114,467,066 108,580,530
TCGA-BH-A18K TCGA-BH-A18K-01A-11R-A12D-07 tumor 152,188,896 145,033,122
TCGA-BH-A18K TCGA-BH-A18K-11A-13R-A12D-07 normal 113,697,894 108,777,175
TCGA-BH-A18L TCGA-BH-A18L-01A-32R-A12D-07 tumor 166,959,318 160,559,369
TCGA-BH-A18L TCGA-BH-A18L-11A-42R-A12D-07 normal 123,907,018 118,773,963
TCGA-BH-A18M TCGA-BH-A18M-01A-11R-A12D-07 tumor 138,539,532 133,534,820
TCGA-BH-A18M TCGA-BH-A18M-11A-33R-A12D-07 normal 117,014,778 112,081,293
TCGA-BH-A18N TCGA-BH-A18N-01A-11R-A12D-07 tumor 142,983,500 137,174,243
TCGA-BH-A18N TCGA-BH-A18N-11A-43R-A12D-07 normal 157,173,156 151,004,445
TCGA-BH-A18P TCGA-BH-A18P-01A-11R-A12D-07 tumor 127,961,746 122,856,373
TCGA-BH-A18P TCGA-BH-A18P-11A-43R-A12D-07 normal 141,933,674 135,157,361
TCGA-BH-A18Q TCGA-BH-A18Q-01A-12R-A12D-07 tumor 121,818,330 116,443,224
TCGA-BH-A18Q TCGA-BH-A18Q-11A-34R-A12D-07 normal 165,063,110 157,994,626
TCGA-BH-A18R TCGA-BH-A18R-01A-11R-A12D-07 tumor 180,017,508 169,411,860
TCGA-BH-A18R TCGA-BH-A18R-11A-42R-A12D-07 normal 172,302,624 165,180,052
TCGA-BH-A18S TCGA-BH-A18S-01A-11R-A12D-07 tumor 147,074,510 139,757,825
TCGA-BH-A18S TCGA-BH-A18S-11A-43R-A12D-07 normal 108,760,074 103,251,901
TCGA-BH-A18U TCGA-BH-A18U-01A-21R-A12D-07 tumor 153,117,930 147,305,950
TCGA-BH-A18U TCGA-BH-A18U-11A-23R-A12D-07 normal 108,106,098 103,639,730
TCGA-BH-A18V TCGA-BH-A18V-01A-11R-A12D-07 tumor 152,271,544 146,188,514
TCGA-BH-A18V TCGA-BH-A18V-11A-52R-A12D-07 normal 121,777,984 115,572,754
TCGA-BH-A1EN TCGA-BH-A1EN-01A-11R-A13Q-07 tumor 168,226,112 160,129,704
TCGA-BH-A1EN TCGA-BH-A1EN-11A-23R-A13Q-07 normal 198,106,966 189,957,185
TCGA-BH-A1ET TCGA-BH-A1ET-01A-11R-A137-07 tumor 234,127,398 218,514,122
TCGA-BH-A1ET TCGA-BH-A1ET-11B-23R-A137-07 normal 204,789,866 190,599,521
TCGA-BH-A1EU TCGA-BH-A1EU-01A-11R-A137-07 tumor 254,079,282 236,090,396
TCGA-BH-A1EU TCGA-BH-A1EU-11A-23R-A137-07 normal 88,875,944 82,217,859
TCGA-BH-A1EV TCGA-BH-A1EV-01A-11R-A137-07 tumor 143,796,230 134,538,432
TCGA-BH-A1EV TCGA-BH-A1EV-11A-24R-A137-07 normal 223,666,660 208,231,188
TCGA-BH-A1F0 TCGA-BH-A1F0-01A-11R-A137-07 tumor 245,563,714 226,590,681
TCGA-BH-A1F0 TCGA-BH-A1F0-11B-23R-A137-07 normal 175,444,638 164,240,206
TCGA-BH-A1F2 TCGA-BH-A1F2-01A-31R-A13Q-07 tumor 182,054,574 165,996,771
TCGA-BH-A1F2 TCGA-BH-A1F2-11A-32R-A13Q-07 normal 211,394,276 197,674,101
TCGA-BH-A1F8 TCGA-BH-A1F8-01A-11R-A13Q-07 tumor 190,032,184 176,361,705
TCGA-BH-A1F8 TCGA-BH-A1F8-11B-21R-A13Q-07 normal 92,792,514 87,956,972
TCGA-BH-A1FC TCGA-BH-A1FC-01A-11R-A13Q-07 tumor 192,081,954 181,597,878
TCGA-BH-A1FC TCGA-BH-A1FC-11A-32R-A13Q-07 normal 89,555,522 84,754,361
TCGA-BH-A1FD TCGA-BH-A1FD-01A-11R-A13Q-07 tumor 179,197,584 169,792,210
TCGA-BH-A1FD TCGA-BH-A1FD-11B-21R-A13Q-07 normal 165,830,618 157,630,877
TCGA-BH-A1FE TCGA-BH-A1FE-01A-11R-A13Q-07 tumor 194,012,334 183,896,043
TCGA-BH-A1FE TCGA-BH-A1FE-11B-14R-A13Q-07 normal 164,068,268 155,541,427
TCGA-BH-A1FG TCGA-BH-A1FG-01A-11R-A13Q-07 tumor 165,311,992 156,482,860
TCGA-BH-A1FG TCGA-BH-A1FG-11B-12R-A13Q-07 normal 155,006,560 145,883,878
TCGA-BH-A1FH TCGA-BH-A1FH-01A-12R-A13Q-07 tumor 173,558,812 160,700,464
TCGA-BH-A1FH TCGA-BH-A1FH-11B-42R-A13Q-07 normal 103,498,436 95,935,851
TCGA-BH-A1FJ TCGA-BH-A1FJ-01A-11R-A13Q-07 tumor 173,646,920 164,562,708
TCGA-BH-A1FJ TCGA-BH-A1FJ-11B-42R-A13Q-07 normal 206,604,094 196,308,892
TCGA-BH-A1FM TCGA-BH-A1FM-01A-11R-A13Q-07 tumor 167,490,818 156,223,648
TCGA-BH-A1FM TCGA-BH-A1FM-11B-23R-A13Q-07 normal 177,663,446 163,165,343
TCGA-BH-A1FN TCGA-BH-A1FN-01A-11R-A13Q-07 tumor 111,066,522 101,202,804
TCGA-BH-A1FN TCGA-BH-A1FN-11A-34R-A13Q-07 normal 194,856,774 179,582,715
TCGA-BH-A1FU TCGA-BH-A1FU-01A-11R-A14D-07 tumor 120,527,438 111,622,679
TCGA-BH-A1FU TCGA-BH-A1FU-11A-23R-A14D-07 normal 96,704,778 89,450,128
TCGA-BH-A203 TCGA-BH-A203-01A-12R-A169-07 tumor 161,989,068 149,573,777
TCGA-BH-A203 TCGA-BH-A203-11A-42R-A169-07 normal 158,460,036 146,317,030
TCGA-BH-A204 TCGA-BH-A204-01A-11R-A157-07 tumor 238,479,610 220,045,943
TCGA-BH-A204 TCGA-BH-A204-11A-53R-A157-07 normal 177,812,166 164,883,210
TCGA-BH-A208 TCGA-BH-A208-01A-11R-A157-07 tumor 155,463,132 144,537,924
TCGA-BH-A208 TCGA-BH-A208-11A-51R-A157-07 normal 174,640,142 160,393,909
TCGA-BH-A209 TCGA-BH-A209-01A-11R-A157-07 tumor 192,061,676 176,312,375
TCGA-BH-A209 TCGA-BH-A209-11A-42R-A157-07 normal 176,182,970 163,675,492
TCGA-E2-A153 TCGA-E2-A153-01A-12R-A12D-07 tumor 102,572,216 96,051,638
TCGA-E2-A153 TCGA-E2-A153-11A-31R-A12D-07 normal 115,937,988 107,568,598
TCGA-E2-A15I TCGA-E2-A15I-01A-21R-A137-07 tumor 146,638,870 135,905,649
TCGA-E2-A15I TCGA-E2-A15I-11A-32R-A137-07 normal 126,867,464 119,500,938
TCGA-E2-A1IG TCGA-E2-A1IG-01A-11R-A144-07 tumor 130,546,032 120,516,018
TCGA-E2-A1IG TCGA-E2-A1IG-11A-22R-A144-07 normal 106,597,786 98,840,798
TCGA-E2-A1L7 TCGA-E2-A1L7-01A-11R-A144-07 tumor 105,931,794 96,897,344
TCGA-E2-A1L7 TCGA-E2-A1L7-11A-33R-A144-07 normal 128,071,058 116,928,826
TCGA-E2-A1LB TCGA-E2-A1LB-01A-11R-A144-07 tumor 128,075,024 116,926,854
TCGA-E2-A1LB TCGA-E2-A1LB-11A-22R-A144-07 normal 131,047,794 118,654,918
TCGA-E2-A1LH TCGA-E2-A1LH-01A-11R-A14D-07 tumor 94,265,648 86,624,226
TCGA-E2-A1LH TCGA-E2-A1LH-11A-22R-A14D-07 normal 103,112,744 95,743,826
TCGA-E2-A1LS TCGA-E2-A1LS-01A-12R-A157-07 tumor 186,637,202 174,114,471
TCGA-E2-A1LS TCGA-E2-A1LS-11A-32R-A157-07 normal 191,241,832 179,721,915
TCGA-E9-A1N4 TCGA-E9-A1N4-01A-11R-A14M-07 tumor 215,147,436 198,666,499
TCGA-E9-A1N4 TCGA-E9-A1N4-11A-33R-A14M-07 normal 183,390,476 166,942,996
TCGA-E9-A1N5 TCGA-E9-A1N5-01A-11R-A14D-07 tumor 101,971,530 94,709,972
TCGA-E9-A1N5 TCGA-E9-A1N5-11A-41R-A14D-07 normal 74,906,248 69,391,419
TCGA-E9-A1N6 TCGA-E9-A1N6-01A-11R-A144-07 tumor 112,531,422 103,416,682
TCGA-E9-A1N6 TCGA-E9-A1N6-11A-32R-A144-07 normal 119,827,390 108,362,462
TCGA-E9-A1N9 TCGA-E9-A1N9-01A-11R-A14D-07 tumor 113,302,316 104,516,149
TCGA-E9-A1N9 TCGA-E9-A1N9-11A-71R-A14D-07 normal 144,989,558 133,098,692
TCGA-E9-A1NA TCGA-E9-A1NA-01A-11R-A144-07 tumor 170,669,660 157,851,142
TCGA-E9-A1NA TCGA-E9-A1NA-11A-33R-A144-07 normal 140,931,424 131,089,817
TCGA-E9-A1ND TCGA-E9-A1ND-01A-11R-A144-07 tumor 110,274,864 101,236,384
TCGA-E9-A1ND TCGA-E9-A1ND-11A-43R-A144-07 normal 123,287,918 114,680,450
TCGA-E9-A1NF TCGA-E9-A1NF-01A-11R-A14D-07 tumor 105,557,758 97,430,054
TCGA-E9-A1NF TCGA-E9-A1NF-11A-73R-A14D-07 normal 126,168,132 116,073,482
TCGA-E9-A1NG TCGA-E9-A1NG-01A-21R-A14M-07 tumor 177,755,906 168,118,165
TCGA-E9-A1NG TCGA-E9-A1NG-11A-52R-A14M-07 normal 126,386,434 119,020,592
TCGA-E9-A1R7 TCGA-E9-A1R7-01A-11R-A14M-07 tumor 153,109,554 140,820,485
TCGA-E9-A1R7 TCGA-E9-A1R7-11A-42R-A14M-07 normal 152,414,992 140,684,925
TCGA-E9-A1RB TCGA-E9-A1RB-01A-11R-A157-07 tumor 207,882,708 192,590,384
TCGA-E9-A1RB TCGA-E9-A1RB-11A-33R-A157-07 normal 193,113,956 179,180,608
TCGA-E9-A1RC TCGA-E9-A1RC-01A-11R-A157-07 tumor 214,169,878 197,839,922
TCGA-E9-A1RC TCGA-E9-A1RC-11A-33R-A157-07 normal 191,561,504 178,905,182
TCGA-E9-A1RD TCGA-E9-A1RD-01A-11R-A157-07 tumor 205,930,788 190,015,708
TCGA-E9-A1RD TCGA-E9-A1RD-11A-33R-A157-07 normal 195,249,518 181,348,145
TCGA-E9-A1RF TCGA-E9-A1RF-01A-11R-A157-07 tumor 178,912,742 163,605,237
TCGA-E9-A1RF TCGA-E9-A1RF-11A-32R-A157-07 normal 164,660,444 151,798,290
TCGA-E9-A1RH TCGA-E9-A1RH-01A-21R-A169-07 tumor 175,787,780 163,603,545
TCGA-E9-A1RH TCGA-E9-A1RH-11A-34R-A169-07 normal 161,791,896 151,350,803
TCGA-E9-A1RI TCGA-E9-A1RI-01A-11R-A169-07 tumor 168,637,356 159,271,831
TCGA-E9-A1RI TCGA-E9-A1RI-11A-41R-A169-07 normal 179,610,576 170,205,380
TCGA-GI-A2C8 TCGA-GI-A2C8-01A-11R-A16F-07 tumor 176,256,310 166,675,701
TCGA-GI-A2C8 TCGA-GI-A2C8-11A-22R-A16F-07 normal 202,277,226 191,832,376
TCGA-A7-A13E TCGA-A7-A13E-01A-11R-A12P-07 tumor 120,076,084 111,783,860
TCGA-A7-A13E TCGA-A7-A13E-11A-61R-A12P-07 normal 120,449,976 114,430,146
TCGA-A7-A13F TCGA-A7-A13F-01A-11R-A12P-07 tumor 131,056,814 123,242,350
TCGA-A7-A13F TCGA-A7-A13F-11A-42R-A12P-07 normal 127,553,008 121,780,335
TCGA-BH-A0AU TCGA-BH-A0AU-01A-11R-A12P-07 tumor 121,550,734 113,655,563
TCGA-BH-A0AU TCGA-BH-A0AU-11A-11R-A12P-07 normal 130,132,628 123,851,495
TCGA-BH-A0BZ TCGA-BH-A0BZ-01A-31R-A12P-07 tumor 167,950,316 158,664,683
TCGA-BH-A0BZ TCGA-BH-A0BZ-11A-61R-A12P-07 normal 154,848,992 148,308,396
TCGA-BH-A0DL TCGA-BH-A0DL-01A-11R-A115-07 tumor 185,570,112 169,925,764
TCGA-BH-A0DL TCGA-BH-A0DL-11A-13R-A115-07 normal 175,130,980 163,873,195
TCGA-BH-A0H5 TCGA-BH-A0H5-01A-21R-A115-07 tumor 143,640,562 133,696,697
TCGA-BH-A0H5 TCGA-BH-A0H5-11A-62R-A115-07 normal 131,059,146 122,391,023
TCGA-BH-A1EO TCGA-BH-A1EO-01A-11R-A137-07 tumor 88,872,062 85,203,628
TCGA-BH-A1EO TCGA-BH-A1EO-11A-31R-A137-07 normal 244,626,096 234,691,096
TCGA-BH-A1EW TCGA-BH-A1EW-01A-11R-A137-07 tumor 133,391,052 127,983,747
TCGA-BH-A1EW TCGA-BH-A1EW-11B-33R-A137-07 normal 240,913,074 228,724,584
TCGA-BH-A1F6 TCGA-BH-A1F6-01A-11R-A13Q-07 tumor 110,977,144 105,583,284
TCGA-BH-A1F6 TCGA-BH-A1F6-11B-94R-A13Q-07 normal 202,110,474 193,566,680
TCGA-BH-A1FB TCGA-BH-A1FB-01A-11R-A13Q-07 tumor 180,440,672 169,385,607
TCGA-BH-A1FB TCGA-BH-A1FB-11A-33R-A13Q-07 normal 108,300,026 102,763,540
TCGA-BH-A1FR TCGA-BH-A1FR-01A-11R-A13Q-07 tumor 102,074,002 97,616,716
TCGA-BH-A1FR TCGA-BH-A1FR-11B-42R-A13Q-07 normal 110,425,192 101,333,217
TCGA-E2-A158 TCGA-E2-A158-01A-11R-A12D-07 tumor 164,123,392 155,384,437
TCGA-E2-A158 TCGA-E2-A158-11A-22R-A12D-07 normal 95,565,186 91,134,922
TCGA-E2-A15M TCGA-E2-A15M-01A-11R-A12D-07 tumor 252,203,574 237,341,949
TCGA-E2-A15M TCGA-E2-A15M-11A-22R-A12D-07 normal 116,152,434 110,797,328

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