bcb894654ac7efb92a8c41a3ad4ffbc8d486e862
NOTCH2.md
| ... | ... | @@ -8,7 +8,6 @@ timeline |
| 8 | 8 | 2008-07-01 : Troen : DLBCL |
| 9 | 9 | 2012-08-27 : Rossi : MZL |
| 10 | 10 | 2013-11-05 : Bea : MCL |
| 11 | - 2019-09-26 : Panea : BL |
|
| 12 | 11 | ``` |
| 13 | 12 | |
| 14 | 13 | ## Relevance tier by entity |
| ... | ... | @@ -16,7 +15,6 @@ timeline |
| 16 | 15 | |Entity|Tier|Description | |
| 17 | 16 | |:------:|:----:|--------------------------------------| |
| 18 | 17 | ||1|high-confidence MZL gene| |
| 19 | -| |2 |relevance in BL not firmly established| |
|
| 20 | 18 | | |1 |high-confidence DLBCL gene | |
| 21 | 19 | | |1 |high-confidence MCL gene | |
| 22 | 20 | |
| ... | ... | @@ -24,9 +22,6 @@ timeline |
| 24 | 22 | |
| 25 | 23 | |Entity|source |frequency (%)| |
| 26 | 24 | |:------:|:---------------------:|:-------------:| |
| 27 | -|BL |GAMBL genomes+capture| 1.15 | |
|
| 28 | -|BL |Thomas cohort | 0.00 | |
|
| 29 | -|BL |Panea cohort | 5.00 | |
|
| 30 | 25 | |DLBCL |GAMBL genomes | 5.74 | |
| 31 | 26 | |DLBCL |Schmitz cohort |11.28 | |
| 32 | 27 | |DLBCL |Reddy cohort | 3.70 | |
| ... | ... | @@ -69,4 +64,4 @@ View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/N |
| 69 | 64 | 1. Trøen G, Wlodarska I, Warsame A, Hernández Llodrà S, De Wolf-Peeters C, Delabie J. NOTCH2 mutations in marginal zone lymphoma. Haematologica. 2008 Jul;93(7):1107–1109. PMID: 18508802 |
| 70 | 65 | 2. Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V, Monti S, Vaisitti T, Arruga F, Famà R, Ciardullo C, Greco M, Cresta S, Piranda D, Holmes A, Fabbri G, Messina M, Rinaldi A, Wang J, Agostinelli C, Piccaluga PP, Lucioni M, Tabbò F, Serra R, Franceschetti S, Deambrogi C, Daniele G, Gattei V, Marasca R, Facchetti F, Arcaini L, Inghirami G, Bertoni F, Pileri SA, Deaglio S, Foà R, Dalla-Favera R, Pasqualucci L, Rabadan R, Gaidano G. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med. 2012 Aug 27;209(9):1537–1551. PMCID: PMC3428941 |
| 71 | 66 | 3. Beà S, Valdés-Mas R, Navarro A, Salaverria I, Martín-Garcia D, Jares P, Giné E, Pinyol M, Royo C, Nadeu F, Conde L, Juan M, Clot G, Vizán P, Croce LD, Puente DA, López-Guerra M, Moros A, Roue G, Aymerich M, Villamor N, Colomo L, Martínez A, Valera A, Martín-Subero JI, Amador V, Hernández L, Rozman M, Enjuanes A, Forcada P, Muntañola A, Hartmann EM, Calasanz MJ, Rosenwald A, Ott G, Hernández-Rivas JM, Klapper W, Siebert R, Wiestner A, Wilson WH, Colomer D, López-Guillermo A, López-Otín C, Puente XS, Campo E. Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. PNAS. 2013 Nov 5;110(45):18250–18255. PMID: 24145436 |
| 72 | -4. Panea R, Love C, Shingleton JR, Reddy A, Bailey J, Moormann A, Otieno J, Ong’echa J, Oduor C, Schroêder K, Masalu N, Chao N, Agajanian M, Major M, Fedoriw Y, Richards K, Rymkiewicz G, Miles R, Alobeid B, Bhagat G, Flowers C, Ondrejka S, Hsi E, Choi W, Au-Yeung R, Hartmann W, Lenz G, Meyerson H, Lin YY, Zhuang Y, Luftig M, Waldrop A, Dave T, Thakkar D, Sahay H, Li G, Palus B, Seshadri V, Kim S, Gascoyne R, Levy S, Mukhopadhyay M, Dunson D, Dave S. The whole genome landscape of Burkitt lymphoma subtypes. Blood. 2019; |
|
| 67 | + |
papers/paneaWholeGenomeLandscape2019.md
| ... | ... | @@ -8,7 +8,7 @@ bibliography: 'morinlab.bib' |
| 8 | 8 | |
| 9 | 9 | |Entity| Tier 1 genes| Tier 2 genes| |
| 10 | 10 | |:-:|:-:|:-:| |
| 11 | -|BL|4|42| |
|
| 11 | +|BL|4|41| |
|
| 12 | 12 | ```mermaid |
| 13 | 13 | --- |
| 14 | 14 | config: |
| ... | ... | @@ -24,8 +24,8 @@ config: |
| 24 | 24 | sankey-beta |
| 25 | 25 | This study, New Tier 1, 4 |
| 26 | 26 | New Tier 1, BL Tier 1, 4 |
| 27 | -This study, New Tier 2, 42 |
|
| 28 | -New Tier 2, BL Tier 2, 42 |
|
| 27 | +This study, New Tier 2, 41 |
|
| 28 | +New Tier 2, BL Tier 2, 41 |
|
| 29 | 29 | All other BL studies, BL Tier 1, 25 |
| 30 | 30 | All other BL studies, BL Tier 2, 111 |
| 31 | 31 | ``` |
| ... | ... | @@ -68,7 +68,6 @@ All other BL studies, BL Tier 2, 111 |
| 68 | 68 | |[MCL1](../MCL1)|2 |★ ★ ★ ★ ☆| |
| 69 | 69 | |[MME](../MME)|2 |★ ☆ ☆ ☆ ☆| |
| 70 | 70 | |[MTOR](../MTOR)|2 |★ ☆ ☆ ☆ ☆| |
| 71 | -|[NOTCH2](../NOTCH2)|2 |☆ ☆ ☆ ☆ ☆| |
|
| 72 | 71 | |[PABPC4L](../PABPC4L)|2 |☆ ☆ ☆ ☆ ☆| |
| 73 | 72 | |[PCDHA11](../PCDHA11)|2 |☆ ☆ ☆ ☆ ☆| |
| 74 | 73 | |[PDZRN3](../PDZRN3)|2 |☆ ☆ ☆ ☆ ☆| |
papers/paneaWholeGenomeLandscape2019.pdf
papers/paneaWholeGenomeLandscape2019_tmp.html
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| 346 | - font-size: inherit;
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| 347 | -}
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| 348 | -
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| 349 | -/* Page Break : use <div class="page"/> to insert page break
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| 350 | --------------------------------------------------------- */
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| 351 | -.page {
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| 352 | - page-break-after: always;
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| 353 | -}
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| 354 | - |
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| 355 | -</style> |
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| 356 | -
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| 357 | -<script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
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| 358 | -</head>
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| 359 | -<body>
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| 360 | - <script>
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| 361 | - mermaid.initialize({
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| 362 | - startOnLoad: true,
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| 363 | - theme: document.body.classList.contains('vscode-dark') || document.body.classList.contains('vscode-high-contrast')
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| 364 | - ? 'dark'
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| 365 | - : 'default'
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| 366 | - });
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| 367 | - </script>
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| 368 | -<h1 id="paneawholegenomelandscape2019">@paneaWholeGenomeLandscape2019</h1> |
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| 369 | -<h2 id="summary-of-novel-genes">Summary of novel genes</h2> |
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| 370 | -<table> |
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| 371 | -<thead> |
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| 372 | -<tr> |
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| 373 | -<th style="text-align:center">Entity</th> |
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| 374 | -<th style="text-align:center">Tier 1 genes</th> |
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| 375 | -<th style="text-align:center">Tier 2 genes</th> |
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| 376 | -</tr> |
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| 377 | -</thead> |
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| 378 | -<tbody> |
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| 379 | -<tr> |
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| 380 | -<td style="text-align:center">BL</td> |
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| 381 | -<td style="text-align:center">4</td> |
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| 382 | -<td style="text-align:center">42</td> |
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| 383 | -</tr> |
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| 384 | -</tbody> |
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| 385 | -</table> |
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| 386 | -<pre><code class="language-mermaid"><div class="mermaid">--- |
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| 387 | -config: |
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| 388 | - sankey: |
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| 389 | - showValues: true |
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| 390 | - linkColor: target |
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| 391 | - width: 600 |
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| 392 | - height: 300 |
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| 393 | - nodeAlignment: right |
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| 394 | - prefix: '(' |
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| 395 | - suffix: ' genes)' |
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| 396 | ---- |
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| 397 | -sankey-beta |
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| 398 | -This study, New Tier 1, 4 |
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| 399 | -New Tier 1, BL Tier 1, 4 |
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| 400 | -This study, New Tier 2, 42 |
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| 401 | -New Tier 2, BL Tier 2, 42 |
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| 402 | -All other BL studies, BL Tier 1, 25 |
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| 403 | -All other BL studies, BL Tier 2, 111 |
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| 404 | -</div></code></pre> |
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| 405 | -<h2 id="novel-genes-reported-in-this-study">Novel genes reported in this study</h2> |
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| 406 | -<h3 id="tier-1">Tier 1</h3> |
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| 407 | -<table> |
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| 408 | -<thead> |
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| 409 | -<tr> |
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| 410 | -<th style="text-align:left">New gene</th> |
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| 411 | -<th style="text-align:center">BL tier</th> |
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| 412 | -</tr> |
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| 413 | -</thead> |
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| 414 | -<tbody> |
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| 415 | -<tr> |
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| 416 | -<td style="text-align:left"><a href="../BMP7">BMP7</a></td> |
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| 417 | -<td style="text-align:center">1</td> |
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| 418 | -</tr> |
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| 419 | -<tr> |
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| 420 | -<td style="text-align:left"><a href="../EIF4A1">EIF4A1</a></td> |
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| 421 | -<td style="text-align:center">1</td> |
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| 422 | -</tr> |
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| 423 | -<tr> |
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| 424 | -<td style="text-align:left"><a href="../EPPK1">EPPK1</a></td> |
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| 425 | -<td style="text-align:center">1</td> |
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| 426 | -</tr> |
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| 427 | -<tr> |
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| 428 | -<td style="text-align:left"><a href="../HNRNPU">HNRNPU</a></td> |
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| 429 | -<td style="text-align:center">1</td> |
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| 430 | -</tr> |
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| 431 | -</tbody> |
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| 432 | -</table> |
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| 433 | -<h3 id="tier-2">Tier 2</h3> |
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| 434 | -<table> |
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| 435 | -<thead> |
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| 436 | -<tr> |
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| 437 | -<th style="text-align:left">New gene</th> |
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| 438 | -<th style="text-align:center">BL tier</th> |
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| 439 | -<th style="text-align:center">Rating of reviewed variants</th> |
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| 440 | -</tr> |
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| 441 | -</thead> |
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| 442 | -<tbody> |
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| 443 | -<tr> |
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| 444 | -<td style="text-align:left"><a href="../ALPK2">ALPK2</a></td> |
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| 445 | -<td style="text-align:center">2</td> |
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| 446 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
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| 447 | -</tr> |
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| 448 | -<tr> |
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| 449 | -<td style="text-align:left"><a href="../CD79B">CD79B</a></td> |
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| 450 | -<td style="text-align:center">2</td> |
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| 451 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 452 | -</tr> |
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| 453 | -<tr> |
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| 454 | -<td style="text-align:left"><a href="../CD83">CD83</a></td> |
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| 455 | -<td style="text-align:center">2</td> |
|
| 456 | -<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 457 | -</tr> |
|
| 458 | -<tr> |
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| 459 | -<td style="text-align:left"><a href="../CTCF">CTCF</a></td> |
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| 460 | -<td style="text-align:center">2</td> |
|
| 461 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 462 | -</tr> |
|
| 463 | -<tr> |
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| 464 | -<td style="text-align:left"><a href="../CXCR4">CXCR4</a></td> |
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| 465 | -<td style="text-align:center">2</td> |
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| 466 | -<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 467 | -</tr> |
|
| 468 | -<tr> |
|
| 469 | -<td style="text-align:left"><a href="../DNMT1">DNMT1</a></td> |
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| 470 | -<td style="text-align:center">2</td> |
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| 471 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 472 | -</tr> |
|
| 473 | -<tr> |
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| 474 | -<td style="text-align:left"><a href="../DTX1">DTX1</a></td> |
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| 475 | -<td style="text-align:center">2</td> |
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| 476 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 477 | -</tr> |
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| 478 | -<tr> |
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| 479 | -<td style="text-align:left"><a href="../ETS1">ETS1</a></td> |
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| 480 | -<td style="text-align:center">2</td> |
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| 481 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
|
| 482 | -</tr> |
|
| 483 | -<tr> |
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| 484 | -<td style="text-align:left"><a href="../FZD3">FZD3</a></td> |
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| 485 | -<td style="text-align:center">2</td> |
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| 486 | -<td style="text-align:center">★ ☆ ☆ ☆ ☆</td> |
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| 487 | -</tr> |
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| 488 | -<tr> |
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| 489 | -<td style="text-align:left"><a href="../HIST1H1C">HIST1H1C</a></td> |
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| 490 | -<td style="text-align:center">2</td> |
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| 491 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 492 | -</tr> |
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| 493 | -<tr> |
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| 494 | -<td style="text-align:left"><a href="../HIST1H2AG">HIST1H2AG</a></td> |
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| 495 | -<td style="text-align:center">2</td> |
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| 496 | -<td style="text-align:center">★ ★ ☆ ☆ ☆</td> |
|
| 497 | -</tr> |
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| 498 | -<tr> |
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| 499 | -<td style="text-align:left"><a href="../HIST1H2AM">HIST1H2AM</a></td> |
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| 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="../HIST1H2BK">HIST1H2BK</a></td> |
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| 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="../HIST1H3D">HIST1H3D</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="../HIST1H3H">HIST1H3H</a></td> |
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| 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="../HIST1H3I">HIST1H3I</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="../HIST1H3J">HIST1H3J</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="../HIST1H4J">HIST1H4J</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="../IGLL5">IGLL5</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="../IKZF3">IKZF3</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="../IRF8">IRF8</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="../KCNK10">KCNK10</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="../MCL1">MCL1</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="../MME">MME</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="../MTOR">MTOR</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="../NOTCH2">NOTCH2</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="../PABPC4L">PABPC4L</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="../PCDHA11">PCDHA11</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="../PDZRN3">PDZRN3</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="../PIK3R1">PIK3R1</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="../PLCG2">PLCG2</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="../PXDNL">PXDNL</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="../RAC2">RAC2</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="../RNF144B">RNF144B</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="../SNTB2">SNTB2</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="../SP3">SP3</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="../SYNCRIP">SYNCRIP</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="../TET2">TET2</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="../WDR7">WDR7</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="../WNK2">WNK2</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="../ZFP36L1">ZFP36L1</a></td> |
|
| 645 | -<td style="text-align:center">2</td> |
|
| 646 | -<td style="text-align:center">☆ ☆ ☆ ☆ ☆</td> |
|
| 647 | -</tr> |
|
| 648 | -</tbody> |
|
| 649 | -</table> |
|
| 650 | -<h1 id="details">Details</h1> |
|
| 651 | -
|
|
| 652 | -</body>
|
|
| 653 | -</html>
|