Table 1.

Table 1A.

Enrichment of significant probes in all probes associated with young L1P lineages. Highlighted in bold are the primate L1P lineages that appear in post-baboon species. The 15,587 probes are the most significant probes characterized in the Supplementary Table S3. Enrichment is calculated based on all 339,314 probes in the microarray. Hypergeometric test score is recorded as well. The two highest enrichment values and two highest p-values are highlighted in bold.

Table 1B.

A continuation of the table from A. For selected families of L1PAs discussed in Table 1A we tried to address the issue whether the statistically significant members (Supplementary table S3) of L1 are more homologous to a promoter region of an active i.e. intact and relatively young, full length Line1 element.

A consensus promoter region was obtained from one of the L1HS characterized by L1Base as full lentgth and active. To generate this table, the alignment of the 700 bases long promoter region was performed against all members of each lineages and against subset of significant members of each of the lineages. Software BLAT and parameters designated to result in 80% homology (-minIdentity=80 -tileSize=10) were used. The count of alignments per lineage was recorded in the table. The “%” columns show the percentage of all elements in the group (either all repeats or subset of significant repeats only) for which a BLAT alignment was found. Note that the percentage does not reflect on sequence conservation, but is a mere statement that an alignment using BLAT and the specified parameters is possible for a fraction of sequences in a group. Subsequently, a hypergeometric test was used to provide statistical significance between the count of alignments in an entire group and only significant members of the group.

Table 1A. Enrichment of significant probes in all probes associated with young L1P lineages.
Family	TOTAL GENOMIC		ALL PROBED		15,587 Most Significant Probes					Length Selection
	N	median length	N	median length	exp	obs	obs/ exp	hyper-geo pval	median length
FLI-L1	145	8,047	87	6,029	4	9	2.252	6.61E-03	6,028	(1)
ORF2-L1	103	8,047	91	6,026	4	13	3.110	7.00E-05	6,026	0
L1HS	1696	987	294	6,025	14	43	3.184	7.25E-12	6,026	2
L1PA2	4666	771	727	6,024	33	115	3.444	3.56E-31	6,023	(1)
L1PA3	10281	952	1070	6,031	49	226	4.598	2.19E-83	6,031	1
L1PA4	11462	713	540	6,130	25	118	4.757	2.80E-46	6,132	2
L1PA5	10904	623	328	5,659	15	46	3.053	6.91E-12	6,115	457
L1PA6	5617	888	169	2,600	8	13	1.675	2.46E-02	4,076	1,476
L1PA7	12334	768	245	1,018	11	23	2.044	4.46E-04	469	(549)
L1PA8	7715	394	159	328	7	20	2.738	1.44E-05	275	(54)
L1PA8A	2210	707	72	677	3	8	2.419	5.65E-03	499	(178)
L1PA10	6962	474	146	676	7	8	1.193	2.30E-01	1,217	542
L1PA11	3886	511	76	601	3	5	1.432	1.36E-01	1,278	678
L1PA12	2320	679	59	644	3	3	1.107	2.87E-01	372	(272)
L1PA13	10722	457	201	503	9	13	1.408	8.12E-02	532	29
L1PA14	3561	558	66	557	3	7	2.309	1.06E-02	337	(220)
L1PA15	8233	547	173	502	8	16	2.013	2.73E-03	450	(52)
L1PA15-16	1201	727	32	331	1	3	2.041	5.75E-02	224	(107)
L1PA16	13098	482	247	489	11	22	1.939	1.15E-03	488	(1)
L1PA17	4722	368	114	368	5	4	0.764	6.05E-01	560	192

Table 1B. Increase of L1HS promoter homology in L1P members with significantly altered methylation patterns.
Family	TOTAL GENOMIC	ALL PROBED			15,587 Most Significant Probes			Improvement in count of alignments	Hyper- geo pval
	N	N	promoter alignments	%	N	promoter alignments	%
FLI-L1	145	87	86	98.85%	9	9	100.00%	1.15%	0.00E+00
L1HS	1696	294	280	95.24%	43	43	100.00%	4.76%	0.00E+00
L1PA2	4666	727	672	92.43%	115	111	96.52%	4.09%	1.53E-02
L1PA3	10281	1070	972	90.84%	226	218	96.46%	5.62%	8.39E-05
L1PA4	11462	540	429	79.44%	118	107	90.68%	11.23%	7.57E-05
L1PA5	10904	328	178	54.27%	46	37	80.43%	26.17%	1.62E-05
L1PA6	5617	169	62	36.69%	13	8	61.54%	24.85%	1.41E-02
L1PA7	12334	245	32	13.06%	23	3	13.04%	(0.02%)	3.25E-01
L1PA8	7715	159	8	5.03%	20	0	0.00%	(5.03%)	6.68E-01