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 |