f3502fdac7d7142526bf71b2fbab0faa77eb9e86
papers/paneaWholeGenomeLandscape2019.md
| ... | ... | @@ -43,11 +43,24 @@ All other BL studies, BL Tier 2, 111 |
| 43 | 43 | ### Tier 2 |
| 44 | 44 | |New gene|BL tier|Rating of reviewed variants|QC outcome| |
| 45 | 45 | |:-|:-:|:-:|:-:| |
| 46 | +|[CD83](../CD83)|2 | ★ ★ ★ ☆ ☆|**Pass**| |
|
| 47 | +|[CXCR4](../CXCR4)|2 | ★ ★ ★ ★ ☆|**Pass**| |
|
| 48 | +|[HIST1H3I](../HIST1H3I)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 49 | +|[HIST1H4J](../HIST1H4J)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 50 | +|[IGLL5](../IGLL5)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 51 | +|[IKZF3](../IKZF3)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 52 | +|[IRF8](../IRF8)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 53 | +|[MCL1](../MCL1)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 54 | +|[HIST1H3D](../HIST1H3D)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 55 | +|[WNK2](../WNK2)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 56 | +|[ZFP36L1](../ZFP36L1)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 57 | +|[RNF144B](../RNF144B)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 58 | + |
|
| 46 | 59 | |[ALPK2](../ALPK2)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
| 47 | 60 | |[CD79B](../CD79B)|2 | ★ ★ ☆ ☆ ☆|**Fail**| |
| 48 | -|[CD83](../CD83)|2 | ★ ★ ★ ☆ ☆|**Pass**| |
|
| 61 | + |
|
| 49 | 62 | |[CTCF](../CTCF)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
| 50 | -|[CXCR4](../CXCR4)|2 | ★ ★ ★ ★ ☆|**Pass**| |
|
| 63 | + |
|
| 51 | 64 | |[DNMT1](../DNMT1)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
| 52 | 65 | |[DTX1](../DTX1)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
| 53 | 66 | |[ETS1](../ETS1)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
| ... | ... | @@ -56,16 +69,13 @@ All other BL studies, BL Tier 2, 111 |
| 56 | 69 | |[HIST1H2AG](../HIST1H2AG)|2 | ★ ★ ☆ ☆ ☆|**Fail**| |
| 57 | 70 | |[HIST1H2AM](../HIST1H2AM)|2 | ☆ ☆ ☆ ☆ ☆|**Fail**| |
| 58 | 71 | |[HIST1H2BK](../HIST1H2BK)|2 | ★ ☆ ☆ ☆ ☆|**Fail**| |
| 59 | -|[HIST1H3D](../HIST1H3D)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 72 | + |
|
| 60 | 73 | |[HIST1H3H](../HIST1H3H)|2 |☆ ☆ ☆ ☆ ☆|**Fail**| |
| 61 | -|[HIST1H3I](../HIST1H3I)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 74 | + |
|
| 62 | 75 | |[HIST1H3J](../HIST1H3J)|2 |☆ ☆ ☆ ☆ ☆|**Fail**| |
| 63 | -|[HIST1H4J](../HIST1H4J)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 64 | -|[IGLL5](../IGLL5)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 65 | -|[IKZF3](../IKZF3)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 66 | -|[IRF8](../IRF8)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 76 | + |
|
| 67 | 77 | |[KCNK10](../KCNK10)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
| 68 | -|[MCL1](../MCL1)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 78 | + |
|
| 69 | 79 | |[MME](../MME)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
| 70 | 80 | |[MTOR](../MTOR)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
| 71 | 81 | |[PABPC4L](../PABPC4L)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
| ... | ... | @@ -74,12 +84,9 @@ All other BL studies, BL Tier 2, 111 |
| 74 | 84 | |[PIK3R1](../PIK3R1)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
| 75 | 85 | |[PLCG2](../PLCG2)|2 |★ ★ ★ ☆ ☆|**Pass**| |
| 76 | 86 | |[PXDNL](../PXDNL)|2 |★ ☆ ☆ ☆ ☆|**Fail**| |
| 77 | -|[RNF144B](../RNF144B)|2 |★ ★ ★ ☆ ☆|**Pass**| |
|
| 87 | + |
|
| 78 | 88 | |[SNTB2](../SNTB2)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
| 79 | 89 | |[WDR7](../WDR7)|2 |★ ★ ☆ ☆ ☆|**Fail**| |
| 80 | -|[WNK2](../WNK2)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 81 | -|[ZFP36L1](../ZFP36L1)|2 |★ ★ ★ ★ ☆|**Pass**| |
|
| 82 | - |
|
| 83 | 90 | |
| 84 | 91 | # Details |
| 85 | 92 |
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| 334 | +.emoji {
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| 335 | + height: 1.4em;
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|
| 336 | +}
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| 337 | +
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| 338 | +code {
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| 339 | + font-size: 14px;
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| 340 | + line-height: 19px;
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| 341 | +}
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| 342 | +
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| 343 | +/* for inline code */
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| 344 | +:not(pre):not(.hljs) > code {
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| 345 | + color: #C9AE75; /* Change the old color so it seems less like an error */
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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">36</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, 36 |
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| 401 | +New Tier 2, BL Tier 2, 36 |
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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> |
|
| 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> |
|
| 411 | +<th style="text-align:center">BL tier</th> |
|
| 412 | +</tr> |
|
| 413 | +</thead> |
|
| 414 | +<tbody> |
|
| 415 | +<tr> |
|
| 416 | +<td style="text-align:left"><a href="../BMP7">BMP7</a></td> |
|
| 417 | +<td style="text-align:center">1</td> |
|
| 418 | +</tr> |
|
| 419 | +<tr> |
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| 420 | +<td style="text-align:left"><a href="../EIF4A1">EIF4A1</a></td> |
|
| 421 | +<td style="text-align:center">1</td> |
|
| 422 | +</tr> |
|
| 423 | +<tr> |
|
| 424 | +<td style="text-align:left"><a href="../EPPK1">EPPK1</a></td> |
|
| 425 | +<td style="text-align:center">1</td> |
|
| 426 | +</tr> |
|
| 427 | +<tr> |
|
| 428 | +<td style="text-align:left"><a href="../HNRNPU">HNRNPU</a></td> |
|
| 429 | +<td style="text-align:center">1</td> |
|
| 430 | +</tr> |
|
| 431 | +</tbody> |
|
| 432 | +</table> |
|
| 433 | +<h3 id="tier-2">Tier 2</h3> |
|
| 434 | +<table> |
|
| 435 | +<thead> |
|
| 436 | +<tr> |
|
| 437 | +<th style="text-align:left">New gene</th> |
|
| 438 | +<th style="text-align:center">BL tier</th> |
|
| 439 | +<th style="text-align:center">Rating of reviewed variants</th> |
|
| 440 | +<th style="text-align:center">QC outcome</th> |
|
| 441 | +</tr> |
|
| 442 | +</thead> |
|
| 443 | +<tbody> |
|
| 444 | +<tr> |
|
| 445 | +<td style="text-align:left"><a href="../CD83">CD83</a></td> |
|
| 446 | +<td style="text-align:center">2</td> |
|
| 447 | +<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 448 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 449 | +</tr> |
|
| 450 | +<tr> |
|
| 451 | +<td style="text-align:left"><a href="../CXCR4">CXCR4</a></td> |
|
| 452 | +<td style="text-align:center">2</td> |
|
| 453 | +<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 454 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 455 | +</tr> |
|
| 456 | +<tr> |
|
| 457 | +<td style="text-align:left"><a href="../HIST1H3I">HIST1H3I</a></td> |
|
| 458 | +<td style="text-align:center">2</td> |
|
| 459 | +<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 460 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 461 | +</tr> |
|
| 462 | +<tr> |
|
| 463 | +<td style="text-align:left"><a href="../HIST1H4J">HIST1H4J</a></td> |
|
| 464 | +<td style="text-align:center">2</td> |
|
| 465 | +<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 466 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 467 | +</tr> |
|
| 468 | +<tr> |
|
| 469 | +<td style="text-align:left"><a href="../IGLL5">IGLL5</a></td> |
|
| 470 | +<td style="text-align:center">2</td> |
|
| 471 | +<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 472 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 473 | +</tr> |
|
| 474 | +<tr> |
|
| 475 | +<td style="text-align:left"><a href="../IKZF3">IKZF3</a></td> |
|
| 476 | +<td style="text-align:center">2</td> |
|
| 477 | +<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 478 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 479 | +</tr> |
|
| 480 | +<tr> |
|
| 481 | +<td style="text-align:left"><a href="../IRF8">IRF8</a></td> |
|
| 482 | +<td style="text-align:center">2</td> |
|
| 483 | +<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 484 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 485 | +</tr> |
|
| 486 | +<tr> |
|
| 487 | +<td style="text-align:left"><a href="../MCL1">MCL1</a></td> |
|
| 488 | +<td style="text-align:center">2</td> |
|
| 489 | +<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 490 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 491 | +</tr> |
|
| 492 | +<tr> |
|
| 493 | +<td style="text-align:left"><a href="../HIST1H3D">HIST1H3D</a></td> |
|
| 494 | +<td style="text-align:center">2</td> |
|
| 495 | +<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 496 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 497 | +</tr> |
|
| 498 | +<tr> |
|
| 499 | +<td style="text-align:left"><a href="../WNK2">WNK2</a></td> |
|
| 500 | +<td style="text-align:center">2</td> |
|
| 501 | +<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 502 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 503 | +</tr> |
|
| 504 | +<tr> |
|
| 505 | +<td style="text-align:left"><a href="../ZFP36L1">ZFP36L1</a></td> |
|
| 506 | +<td style="text-align:center">2</td> |
|
| 507 | +<td style="text-align:center">★ ★ ★ ★ ☆</td> |
|
| 508 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 509 | +</tr> |
|
| 510 | +<tr> |
|
| 511 | +<td style="text-align:left"><a href="../RNF144B">RNF144B</a></td> |
|
| 512 | +<td style="text-align:center">2</td> |
|
| 513 | +<td style="text-align:center">★ ★ ★ ☆ ☆</td> |
|
| 514 | +<td style="text-align:center"><strong>Pass</strong></td> |
|
| 515 | +</tr> |
|
| 516 | +</tbody> |
|
| 517 | +</table> |
|
| 518 | +<p>|<a href="../ALPK2">ALPK2</a>|2 | ★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 519 | +|<a href="../CD79B">CD79B</a>|2 | ★ ★ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 520 | +<p>|<a href="../CTCF">CTCF</a>|2 | ★ ☆ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 521 | +<p>|<a href="../DNMT1">DNMT1</a>|2 | ★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 522 | +|<a href="../DTX1">DTX1</a>|2 | ★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 523 | +|<a href="../ETS1">ETS1</a>|2 | ★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 524 | +|<a href="../FZD3">FZD3</a>|2 | ★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 525 | +|<a href="../HIST1H1C">HIST1H1C</a>|2 | ★ ★ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 526 | +|<a href="../HIST1H2AG">HIST1H2AG</a>|2 | ★ ★ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 527 | +|<a href="../HIST1H2AM">HIST1H2AM</a>|2 | ☆ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 528 | +|<a href="../HIST1H2BK">HIST1H2BK</a>|2 | ★ ☆ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 529 | +<p>|<a href="../HIST1H3H">HIST1H3H</a>|2 |☆ ☆ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 530 | +<p>|<a href="../HIST1H3J">HIST1H3J</a>|2 |☆ ☆ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 531 | +<p>|<a href="../KCNK10">KCNK10</a>|2 |★ ★ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 532 | +<p>|<a href="../MME">MME</a>|2 |★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 533 | +|<a href="../MTOR">MTOR</a>|2 |★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 534 | +|<a href="../PABPC4L">PABPC4L</a>|2 |★ ★ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 535 | +|<a href="../PCDHA11">PCDHA11</a>|2 |★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 536 | +|<a href="../PDZRN3">PDZRN3</a>|2 |★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 537 | +|<a href="../PIK3R1">PIK3R1</a>|2 |★ ☆ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 538 | +|<a href="../PLCG2">PLCG2</a>|2 |★ ★ ★ ☆ ☆|<strong>Pass</strong>| |
|
| 539 | +|<a href="../PXDNL">PXDNL</a>|2 |★ ☆ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 540 | +<p>|<a href="../SNTB2">SNTB2</a>|2 |★ ★ ☆ ☆ ☆|<strong>Fail</strong>| |
|
| 541 | +|<a href="../WDR7">WDR7</a>|2 |★ ★ ☆ ☆ ☆|<strong>Fail</strong>|</p> |
|
| 542 | +<h1 id="details">Details</h1> |
|
| 543 | +
|
|
| 544 | +</body>
|
|
| 545 | +</html>
|