papers/reddyGeneticFunctionalDrivers2017.md
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@@ -102,7 +102,7 @@ All other DLBCL studies, DLBCL Tier 2, 145
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## See Also
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105
-The primary data supporting each of the mutations reported in this study can be viewed in [IGV reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/)
105
+The primary data supporting each of the mutations reported in this study can be viewed in [IGV reports](https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/)
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# Details
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papers/reddyGeneticFunctionalDrivers2017_tmp.html
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+<h1 id="reddygeneticfunctionaldrivers2017">@reddyGeneticFunctionalDrivers2017</h1>
369
+<h2 id="summary-of-novel-genes">Summary of novel genes</h2>
370
+<table>
371
+<thead>
372
+<tr>
373
+<th style="text-align:center">Entity</th>
374
+<th style="text-align:center">Tier 1 genes</th>
375
+<th style="text-align:center">Tier 2 genes</th>
376
+</tr>
377
+</thead>
378
+<tbody>
379
+<tr>
380
+<td style="text-align:center">DLBCL</td>
381
+<td style="text-align:center">7</td>
382
+<td style="text-align:center">53</td>
383
+</tr>
384
+</tbody>
385
+</table>
386
+<pre><code class="language-mermaid"><div class="mermaid">---
387
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+ prefix: '('
395
+ suffix: ' genes)'
396
+---
397
+sankey-beta
398
+This study, New Tier 1, 7
399
+New Tier 1, DLBCL Tier 1, 7
400
+This study, New Tier 2, 53
401
+New Tier 2, DLBCL Tier 2, 53
402
+All other DLBCL studies, DLBCL Tier 1, 121
403
+All other DLBCL studies, DLBCL Tier 2, 145
404
+</div></code></pre>
405
+<h2 id="novel-genes-reported-in-this-study">Novel genes reported in this study</h2>
406
+<h3 id="tier-1">Tier 1</h3>
407
+<table>
408
+<thead>
409
+<tr>
410
+<th style="text-align:left">New gene</th>
411
+<th style="text-align:center">DLBCL tier</th>
412
+<th style="text-align:center">Rating of reviewed variants</th>
413
+</tr>
414
+</thead>
415
+<tbody>
416
+<tr>
417
+<td style="text-align:left"><a href="../ATM">ATM</a></td>
418
+<td style="text-align:center">1</td>
419
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
420
+</tr>
421
+<tr>
422
+<td style="text-align:left"><a href="../BIRC6">BIRC6</a></td>
423
+<td style="text-align:center">1</td>
424
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
425
+</tr>
426
+<tr>
427
+<td style="text-align:left"><a href="../HIST1H2BC">HIST1H2BC</a></td>
428
+<td style="text-align:center">1</td>
429
+<td style="text-align:center">★ ★ ★ ★ ☆</td>
430
+</tr>
431
+<tr>
432
+<td style="text-align:left"><a href="../HNRNPU">HNRNPU</a></td>
433
+<td style="text-align:center">1</td>
434
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
435
+</tr>
436
+<tr>
437
+<td style="text-align:left"><a href="../SETD1B">SETD1B</a></td>
438
+<td style="text-align:center">1</td>
439
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
440
+</tr>
441
+<tr>
442
+<td style="text-align:left"><a href="../TOX">TOX</a></td>
443
+<td style="text-align:center">1</td>
444
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
445
+</tr>
446
+<tr>
447
+<td style="text-align:left"><a href="../UBE2A">UBE2A</a></td>
448
+<td style="text-align:center">1</td>
449
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
450
+</tr>
451
+</tbody>
452
+</table>
453
+<h3 id="tier-2">Tier 2</h3>
454
+<table>
455
+<thead>
456
+<tr>
457
+<th style="text-align:left">New gene</th>
458
+<th style="text-align:center">DLBCL tier</th>
459
+<th style="text-align:center">Rating of reviewed variants</th>
460
+</tr>
461
+</thead>
462
+<tbody>
463
+<tr>
464
+<td style="text-align:left"><a href="../ANKRD17">ANKRD17</a></td>
465
+<td style="text-align:center">2</td>
466
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
467
+</tr>
468
+<tr>
469
+<td style="text-align:left"><a href="../ARID1B">ARID1B</a></td>
470
+<td style="text-align:center">2</td>
471
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
472
+</tr>
473
+<tr>
474
+<td style="text-align:left"><a href="../ARID5B">ARID5B</a></td>
475
+<td style="text-align:center">2</td>
476
+<td style="text-align:center">★ ★ ★ ★ ☆</td>
477
+</tr>
478
+<tr>
479
+<td style="text-align:left"><a href="../ATR">ATR</a></td>
480
+<td style="text-align:center">2</td>
481
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
482
+</tr>
483
+<tr>
484
+<td style="text-align:left"><a href="../BRINP3">BRINP3</a></td>
485
+<td style="text-align:center">2</td>
486
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
487
+</tr>
488
+<tr>
489
+<td style="text-align:left"><a href="../BTBD3">BTBD3</a></td>
490
+<td style="text-align:center">2</td>
491
+<td style="text-align:center">★ ★ ★ ★ ☆</td>
492
+</tr>
493
+<tr>
494
+<td style="text-align:left"><a href="../CASP8">CASP8</a></td>
495
+<td style="text-align:center">2</td>
496
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
497
+</tr>
498
+<tr>
499
+<td style="text-align:left"><a href="../CBLB">CBLB</a></td>
500
+<td style="text-align:center">2</td>
501
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
502
+</tr>
503
+<tr>
504
+<td style="text-align:left"><a href="../CD22">CD22</a></td>
505
+<td style="text-align:center">2</td>
506
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
507
+</tr>
508
+<tr>
509
+<td style="text-align:left"><a href="../CDC73">CDC73</a></td>
510
+<td style="text-align:center">2</td>
511
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
512
+</tr>
513
+<tr>
514
+<td style="text-align:left"><a href="../CHD1">CHD1</a></td>
515
+<td style="text-align:center">2</td>
516
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
517
+</tr>
518
+<tr>
519
+<td style="text-align:left"><a href="../CHD8">CHD8</a></td>
520
+<td style="text-align:center">2</td>
521
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
522
+</tr>
523
+<tr>
524
+<td style="text-align:left"><a href="../CHST2">CHST2</a></td>
525
+<td style="text-align:center">2</td>
526
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
527
+</tr>
528
+<tr>
529
+<td style="text-align:left"><a href="../DCAF6">DCAF6</a></td>
530
+<td style="text-align:center">2</td>
531
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
532
+</tr>
533
+<tr>
534
+<td style="text-align:left"><a href="../DDX10">DDX10</a></td>
535
+<td style="text-align:center">2</td>
536
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
537
+</tr>
538
+<tr>
539
+<td style="text-align:left"><a href="../DICER1">DICER1</a></td>
540
+<td style="text-align:center">2</td>
541
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
542
+</tr>
543
+<tr>
544
+<td style="text-align:left"><a href="../DNMT3A">DNMT3A</a></td>
545
+<td style="text-align:center">2</td>
546
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
547
+</tr>
548
+<tr>
549
+<td style="text-align:left"><a href="../FOXP1">FOXP1</a></td>
550
+<td style="text-align:center">2</td>
551
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
552
+</tr>
553
+<tr>
554
+<td style="text-align:left"><a href="../FUBP1">FUBP1</a></td>
555
+<td style="text-align:center">2</td>
556
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
557
+</tr>
558
+<tr>
559
+<td style="text-align:left"><a href="../GNAS">GNAS</a></td>
560
+<td style="text-align:center">2</td>
561
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
562
+</tr>
563
+<tr>
564
+<td style="text-align:left"><a href="../GOLGA5">GOLGA5</a></td>
565
+<td style="text-align:center">2</td>
566
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
567
+</tr>
568
+<tr>
569
+<td style="text-align:left"><a href="../HRAS">HRAS</a></td>
570
+<td style="text-align:center">2</td>
571
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
572
+</tr>
573
+<tr>
574
+<td style="text-align:left"><a href="../IKBKB">IKBKB</a></td>
575
+<td style="text-align:center">2</td>
576
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
577
+</tr>
578
+<tr>
579
+<td style="text-align:left"><a href="../JUNB">JUNB</a></td>
580
+<td style="text-align:center">2</td>
581
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
582
+</tr>
583
+<tr>
584
+<td style="text-align:left"><a href="../KCMF1">KCMF1</a></td>
585
+<td style="text-align:center">2</td>
586
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
587
+</tr>
588
+<tr>
589
+<td style="text-align:left"><a href="../LIN54">LIN54</a></td>
590
+<td style="text-align:center">2</td>
591
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
592
+</tr>
593
+<tr>
594
+<td style="text-align:left"><a href="../MAGT1">MAGT1</a></td>
595
+<td style="text-align:center">2</td>
596
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
597
+</tr>
598
+<tr>
599
+<td style="text-align:left"><a href="../MAP4K4">MAP4K4</a></td>
600
+<td style="text-align:center">2</td>
601
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
602
+</tr>
603
+<tr>
604
+<td style="text-align:left"><a href="../MARK1">MARK1</a></td>
605
+<td style="text-align:center">2</td>
606
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
607
+</tr>
608
+<tr>
609
+<td style="text-align:left"><a href="../MCL1">MCL1</a></td>
610
+<td style="text-align:center">2</td>
611
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
612
+</tr>
613
+<tr>
614
+<td style="text-align:left"><a href="../MECOM">MECOM</a></td>
615
+<td style="text-align:center">2</td>
616
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
617
+</tr>
618
+<tr>
619
+<td style="text-align:left"><a href="../MET">MET</a></td>
620
+<td style="text-align:center">2</td>
621
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
622
+</tr>
623
+<tr>
624
+<td style="text-align:left"><a href="../MSH2">MSH2</a></td>
625
+<td style="text-align:center">2</td>
626
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
627
+</tr>
628
+<tr>
629
+<td style="text-align:left"><a href="../MSH6">MSH6</a></td>
630
+<td style="text-align:center">2</td>
631
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
632
+</tr>
633
+<tr>
634
+<td style="text-align:left"><a href="../MYB">MYB</a></td>
635
+<td style="text-align:center">2</td>
636
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
637
+</tr>
638
+<tr>
639
+<td style="text-align:left"><a href="../NCOR1">NCOR1</a></td>
640
+<td style="text-align:center">2</td>
641
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
642
+</tr>
643
+<tr>
644
+<td style="text-align:left"><a href="../NF1">NF1</a></td>
645
+<td style="text-align:center">2</td>
646
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
647
+</tr>
648
+<tr>
649
+<td style="text-align:left"><a href="../NFKB2">NFKB2</a></td>
650
+<td style="text-align:center">2</td>
651
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
652
+</tr>
653
+<tr>
654
+<td style="text-align:left"><a href="../PHF6">PHF6</a></td>
655
+<td style="text-align:center">2</td>
656
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
657
+</tr>
658
+<tr>
659
+<td style="text-align:left"><a href="../PIK3CD">PIK3CD</a></td>
660
+<td style="text-align:center">2</td>
661
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
662
+</tr>
663
+<tr>
664
+<td style="text-align:left"><a href="../PTPN6">PTPN6</a></td>
665
+<td style="text-align:center">2</td>
666
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
667
+</tr>
668
+<tr>
669
+<td style="text-align:left"><a href="../PTPRK">PTPRK</a></td>
670
+<td style="text-align:center">2</td>
671
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
672
+</tr>
673
+<tr>
674
+<td style="text-align:left"><a href="../RARA">RARA</a></td>
675
+<td style="text-align:center">2</td>
676
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
677
+</tr>
678
+<tr>
679
+<td style="text-align:left"><a href="../RUNX1">RUNX1</a></td>
680
+<td style="text-align:center">2</td>
681
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
682
+</tr>
683
+<tr>
684
+<td style="text-align:left"><a href="../SETD5">SETD5</a></td>
685
+<td style="text-align:center">2</td>
686
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
687
+</tr>
688
+<tr>
689
+<td style="text-align:left"><a href="../SYK">SYK</a></td>
690
+<td style="text-align:center">2</td>
691
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
692
+</tr>
693
+<tr>
694
+<td style="text-align:left"><a href="../TGFBR2">TGFBR2</a></td>
695
+<td style="text-align:center">2</td>
696
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
697
+</tr>
698
+<tr>
699
+<td style="text-align:left"><a href="../TIPARP">TIPARP</a></td>
700
+<td style="text-align:center">2</td>
701
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
702
+</tr>
703
+<tr>
704
+<td style="text-align:left"><a href="../WAC">WAC</a></td>
705
+<td style="text-align:center">2</td>
706
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
707
+</tr>
708
+<tr>
709
+<td style="text-align:left"><a href="../YY1">YY1</a></td>
710
+<td style="text-align:center">2</td>
711
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
712
+</tr>
713
+<tr>
714
+<td style="text-align:left"><a href="../ZBTB7A">ZBTB7A</a></td>
715
+<td style="text-align:center">2</td>
716
+<td style="text-align:center">★ ☆ ☆ ☆ ☆</td>
717
+</tr>
718
+<tr>
719
+<td style="text-align:left"><a href="../ZFAT">ZFAT</a></td>
720
+<td style="text-align:center">2</td>
721
+<td style="text-align:center">★ ★ ☆ ☆ ☆</td>
722
+</tr>
723
+<tr>
724
+<td style="text-align:left"><a href="../ZFX">ZFX</a></td>
725
+<td style="text-align:center">2</td>
726
+<td style="text-align:center">★ ★ ★ ☆ ☆</td>
727
+</tr>
728
+</tbody>
729
+</table>
730
+<h2 id="see-also">See Also</h2>
731
+<p>The primary data supporting each of the mutations reported in this study can be viewed in <a href="https://www.bcgsc.ca/downloads/morinlab/GAMBL/Reddy/igv_reports/">IGV reports</a></p>
732
+<h1 id="details">Details</h1>
733
+
734
+</body>
735
+</html>