Table 5

Experimental evaluation

Method meets criteria


Evaluation criteria

Experimental evidence

References

IsoF

GC-P

BASIO

L-S

Consensus


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.

[2,3,18]

No

Partly

No

Partly

Yes


IsoF, IsoFinder; GC-P, GC-Profile; L-S, least-squares.

Schmidt and Frishman Genome Biology 2008 9:R104   doi:10.1186/gb-2008-9-6-r104

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