Supplementary Data.

Donaldson and Gottgens (2006).

ABBREVIATION:
TFBS = Transcription factor binding site

UCSC custom track files:
chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10
chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19
chrX chrY

These files can be downloaded and viewed in the UCSC genome browser (Mouse March 2005). Alternatively the URL for these files can be added to the custom track input box. The address is:

http://hscl.cimr.cam.ac.uk/sup_donaldson06/ucsc_also_human_nodup_noexon_mar05_4track_chrN.bed (where N = chromosome; 1-19, X or Y).

Motif data files:
Complete M.m./P.t. conserved Xie TFBSs
Complete M.m./H.s. conserved Xie TFBSs

Xie TFBSs conserved between M.m./P.t. that are not conserved between M.m./H.s. (filtered)
(filtered to remove TFBSs in exons and only contain those from mouse regions aligned to both chimpanzee and human sequence)
Complete Xie TFBSs conserved between M.m./P.t. (filtered)
(filtered to remove TFBSs in exons and only contain those from mouse regions aligned to both chimpanzee and human sequence)

Mouse gene symbol files:
Files containing the symbols of genes located within (and +/- 25kb flanking) of genome tiles where chimpanzee-mouse TFBSs (not present in mouse-human) are over-represented compared to the entire chimpanzee-mouse TFBS set.
>= 3 fold over median enrichment
>= 6 fold over median enrichment
>= 2 Std Dev enrichment

GoToolBox input files:
The file contain the input files generated by GoToolBox 'Create-Dataset'.
>= 3 fold over median enrichment
>= 6 fold over median enrichment
>= 2 Std Dev enrichment

Summary table of TFBS data for this study:
Candidate TFBSs were identified as outlined in the text. Motif numbers and IUPAC consensus sequences refer to the TFBSs reported by Xie et. al. The name in parenthesis is the best matching TRANSFAC TFBS, as determined by the above study. Numbers of binding sites are shown for each TFBS found in the sequence alignments of mouse-chimpanzee and mouse-human. Also shown are the numbers of candidate TFBSs lost in the human genome together with numbers of genes localised to these TFBSs. Numbers are presented for the total non-redundant dataset (unfiltered) and the final filtered dataset (filtered). M. m = Mus musculus; H. s. = Homo sapiens; P. t. = Pan troglodytes.

Motif	IUPAC string	Conserved TFBSs		P.t. TFBSs not in H.s.
		M.m./P.t. *1	M.m./H.s. *1	Unfiltered *2	Filtered *3
1: NRF-2	RCGCAnGCGY	1137	1311	60	41
2: MYC	CACGTG	12870	13824	562	385
3: ELK-1	SCGGAAGY	3410	3716	3410	1906
4: --	ACTAYRnnnCCCR	386	431	16	11
5: NF-Y	GATTGGY	11724	12160	624	485
6: SP1	GGGCGGR	8848	10244	680	549
7: AP-1	TGAnTCA	85194	87414	2152	1759
8: --	TMTCGCGAnR	253	283	3	2
9: ATF3	TGAYRTCA	15444	16000	389	303
10:YY1	GCCATnTTG	3398	3559	180	138
11: GABP	MGGAAGTG	6911	7213	362	272
12: E12	CAGGTG	97105	101061	5627	4247
13: LEF1	CTTTGT	116849	119762	6749	5323
14: ATF3	TGACGTCA	1446	1566	26	22
15: AP-4	CAGCTG	168758	174850	3800	2834
16: C-ETS-2	RYTTCCTG	29315	30360	1409	1092
17: IRF1	AACTTT	105180	107711	6522	5137
18: SREBP-1	TCAnnTGAY	16135	16588	896	741
19: --	GKCGCn(7)TGAYG	18	19	1	1
20: E4F1	GTGACGY	2412	2626	116	84
21: --	GGAAnCGGAAnY	105	117	6	5
22: --	TGCGCAnK	2496	2776	140	71
23: CHX10	TAATTA	205934	210584	4816	3895
24: MAZ	GGGAGGRR	20902	22637	1434	1150
25: ESRRA	TGACCTY	43545	44548	2506	2012
26: E4BP4	TTAYRTAA	16974	17382	551	465
27: --	TGGn(6)KCCAR	5249	5492	304	229
28: RSRFC4	CTAWWWATA	15942	16359	754	660
29: --	CTTTAAR	60391	61875	3506	2740
30: --	YGCGYRCGC	1185	1456	195	116

NOTES:
*1 = Binding sites that are conserved between aligned genomes
*2 = Non-overlapping binding sites that are present in the chimpanzee genome BUT NOT in the human genome (relative to the mouse genome)
*3 = Motif libraries where sites have been removed that are present in sequence annotated as exons or affected by structural variation