Table 5 |
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|
Experimental evaluation |
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|
Method meets criteria |
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|
|
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|
Evaluation criteria |
Experimental evidence |
References |
IsoF |
GC-P |
BASIO |
L-S |
Consensus |
|
|
|
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|
1. |
Isochore border between the genes MN1 (in the GC rich region) and PITPNB (in the GC poor region) in the human genome |
Replication time during the S phase of the cell cycle |
[30] |
Yes |
Yes |
Yes |
No |
Yes |
|
Early MN1 gene, late PITPNB gene |
||||||||
|
Pause of about 3 hours at isochore border |
||||||||
|
2. |
Isochore border within the KIAA1043 gene in the human genome |
Replication time during the S phase of the cell cycle |
[30] |
Yes |
No |
Yes |
No |
Yes |
|
Long pause at isochore border |
||||||||
|
3. |
Isochore border between the MHC classes II and class III regions |
Replication time during the S phase of the cell cycle |
[17] |
Yes |
Yes |
Yes |
Yes |
Yes |
|
Long pause at isochore border |
||||||||
|
4. |
Typical isochore length and isochore length distribution subject to isochore GC content |
Ultra-centrifugation in combination with fragmentations at different scales. See also theoretical discussions in Constantini et al. |
No |
Partly |
No |
Partly |
Yes |
|
|
|
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|
IsoF, IsoFinder; GC-P, GC-Profile; L-S, least-squares. |
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|
Schmidt and Frishman Genome Biology 2008 9:R104 doi:10.1186/gb-2008-9-6-r104 |
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