Changes in 5b5ea7d: drop

				SP3.md
			
          @@ -1,49 +0,0 @@

          -# SP3

          -

          -## History

          -```mermaid

          -%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%

          -timeline

          -    title Publication timing

          -      2019-09-26 : Panea : BL

          -```

          -

          -## Relevance tier by entity

          -

          -|Entity|Tier|Description                           |

          -|:------:|:----:|--------------------------------------|

          -|![BL](images/icons/BL_tier2.png)    |2   |relevance in BL not firmly established|

          -

          -## Mutation incidence in large patient cohorts (GAMBL reanalysis)

          -

          -|Entity|source               |frequency (%)|

          -|:------:|:---------------------:|:-------------:|

          -|BL    |GAMBL genomes+capture|3.0          |

          -|BL    |Thomas cohort        |2.5          |

          -|BL    |Panea cohort         |5.0          |

          -

          -## Mutation pattern and selective pressure estimates

          -

          -|Entity|aSHM|Significant selection|dN/dS (missense)|dN/dS (nonsense)|

          -|:------:|:----:|:---------------------:|:----------------:|:----------------:|

          -|BL    |No  |No                   |1.249           |16.244          |

          -|DLBCL |No  |No                   |1.085           |25.775          |

          -|FL    |No  |No                   |2.231           |27.201          |

          -

          -

          -

          -View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP3_protein.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP3_protein_hg38.html)

          -

          -![](images/proteinpaint/SP3_NM_003111.svg)

          -

          -View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP3.html)  or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP3_hg38.html)

          -

          -![](images/proteinpaint/SP3.svg)

          -

          -## SP3 Expression

          -![](images/gene_expression/SP3_by_pathology.svg)

          -<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->

          -<!-- BL: paneaWholeGenomeLandscape2019 -->

          -

          -## References

          -1.  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;

...	...	@@ -1,49 +0,0 @@
1		-# SP3
2		-
3		-## History
4		-```mermaid
5		-%%{init: { 'logLevel': 'debug', 'theme': 'dark' } }%%
6		-timeline
7		- title Publication timing
8		- 2019-09-26 : Panea : BL
9		-```
10		-
11		-## Relevance tier by entity
12		-
13		-\|Entity\|Tier\|Description \|
14		-\|:------:\|:----:\|--------------------------------------\|
15		-\|![BL](images/icons/BL_tier2.png) \|2 \|relevance in BL not firmly established\|
16		-
17		-## Mutation incidence in large patient cohorts (GAMBL reanalysis)
18		-
19		-\|Entity\|source \|frequency (%)\|
20		-\|:------:\|:---------------------:\|:-------------:\|
21		-\|BL \|GAMBL genomes+capture\|3.0 \|
22		-\|BL \|Thomas cohort \|2.5 \|
23		-\|BL \|Panea cohort \|5.0 \|
24		-
25		-## Mutation pattern and selective pressure estimates
26		-
27		-\|Entity\|aSHM\|Significant selection\|dN/dS (missense)\|dN/dS (nonsense)\|
28		-\|:------:\|:----:\|:---------------------:\|:----------------:\|:----------------:\|
29		-\|BL \|No \|No \|1.249 \|16.244 \|
30		-\|DLBCL \|No \|No \|1.085 \|25.775 \|
31		-\|FL \|No \|No \|2.231 \|27.201 \|
32		-
33		-
34		-
35		-View coding variants in ProteinPaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP3_protein.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP3_protein_hg38.html)
36		-
37		-![](images/proteinpaint/SP3_NM_003111.svg)
38		-
39		-View all variants in GenomePaint [hg19](https://morinlab.github.io/LLMPP/GAMBL/SP3.html) or [hg38](https://morinlab.github.io/LLMPP/GAMBL/SP3_hg38.html)
40		-
41		-![](images/proteinpaint/SP3.svg)
42		-
43		-## SP3 Expression
44		-![](images/gene_expression/SP3_by_pathology.svg)
45		-<!-- ORIGIN: paneaWholeGenomeLandscape2019 -->
46		-<!-- BL: paneaWholeGenomeLandscape2019 -->
47		-
48		-## References
49		-1. 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;