Table 6.
Limb-Specific Transcription Factors and Homologous ESTs
| SAGE tag | Tag count | Copies per cell | Percent abund. | UniGene ID | Description | Tag matching values | |||||||
| fore | hind | sum | Num | Sum | Count | Fit | |||||||
| General transcription factors | |||||||||||||
| CTCTTATTTT | 2 | 0 | 2 | 0.55 | 0.0015 | 38850 | pre B-cell leukemia transcription factor 1 | 2 | 4 | 3 | 1.00 | ||
| CTGATTTATT | 0 | 2 | 2 | 0.55 | 0.0015 | 7103 | pre B-cell leukemia transcription factor 2 | 5 | 23 | 8 | 0.52 | ||
| CCAAGAAACA | 1 | 0 | 1 | 0.27 | 0.00073 | 4563 | metal response element binding transcription factor 1 | 2 | 5 | 3 | 0.80 | ||
| CATAATAAAT | 0 | 1 | 1 | 0.27 | 0.00073 | 8012 | Mus musculus Ets transcriptions factor Spi-B, partial cds | 4 | 4 | 1 | 1.00 | ||
| GACAAGATGT | 0 | 1 | 1 | 0.27 | 0.00073 | 4795 | transcription factor AP-2 beta | 3 | 9 | 7 | 1.00 | ||
| ACGCCCCGGCT | 1 | 0 | 1 | 0.27 | 0.00073 | 41124 | ESTs, highly similar to transcription factor TFE3 (Homo sapiens) | 1 | 1 | 1 | 1.00 | ||
| TCTCTCATTT | 1 | 0 | 1 | 0.27 | 0.00073 | 25856 | ESTs, moderately similar to AF133123_1 transcription factor IIIC102 (H. sapiens) | 3 | 11 | 9 | 1.00 | ||
| TTTCAGTGGG | 0 | 1 | 1 | 0.27 | 0.00073 | 46503 | M. musculus ets family transcription factor ELF2B1 (ELF2) mRNA, complete cds, alternatively spliced. | 7 | 20 | 8 | 0.70 | ||
| AACAAGAAAG | 1 | 0 | 1 | 0.27 | 0.00073 | 897 | POU domain, class 2, associating factor 1 | 10 | 18 | 7 | 0.89 | ||
| Homeodomain containing | |||||||||||||
| TACGTCTATT | 0 | 26 | 26 | 7.1 | 0.019 | 4832 | paired-like homeodomain transcription factor 1 | 2 | 3 | 2 | 1.00 | ||
| CAGAACAAGT | 7 | 7 | 14 | 3.8 | 0.010 | 4346 | ESTs, highly similar to MOX2_MOUSE HOMEOBOX PROTEIN MOX-2 (M. musculus) | 16 | 23 | 7 | 0.96 | ||
| TCGCCGGGCG | 0 | 14 | 14 | 3.8 | 0.010 | 4832 | paired-like homeodomain transcription factor 1 | 1 | 3 | 2 | 0.67 | ||
| TGAATGTTCG | 2 | 0 | 2 | 0.55 | 0.0015 | 5039 | sine oculis-related homeobox 2 homolog (Drosophila) | 1 | 2 | 2 | 1.00 | ||
| TTATACAGAA | 2 | 0 | 2 | 0.55 | 0.0015 | 1385 | paired-like homeodomain transcription factor 2 | 4 | 4 | 1 | 1.00 | ||
| TCTGTGTATG | 1 | 0 | 1 | 0.27 | 0.00073 | 39039 | iroquois related homeobox 3 (Drosophila) | 19 | 19 | 1 | 1.00 | ||
| TACAGGACTT | 1 | 0 | 1 | 0.27 | 0.00073 | 5194 | distal-less homeobox 3 | 1 | 1 | 1 | 1.00 | ||
| TATCAGTTTT | 0 | 1 | 1 | 0.27 | 0.00073 | 3404 | mesenchyme homeobox 1 | 3 | 3 | 1 | 1.00 | ||
| TATCAGTTTT | 0 | 1 | 1 | 0.27 | 0.00073 | 141812 | ESTs, highly similar to MOX1_MOUSE HOMEOBOX PROTEIN MOX-1 (M. musculus) | 24 | 29 | 5 | 0.97 | ||
| TTGGCTTCTC | 0 | 1 | 1 | 0.27 | 0.00073 | 147618 | EST, moderately similar to HEX1_MOUSE ANTERIOR-RESTRICTED HOMEOBOX PROTEIN (M. musculus) | 1 | 1 | 1 | 1.00 | ||
| ATGGATAGAC | 1 | 0 | 1 | 0.27 | 0.00073 | 153716 | mesenchyme homeobox 2 | 1 | 1 | 1 | 1.00 | ||
| Zinc finger containing | |||||||||||||
| CGATCAGCAA | 4 | 0 | 4 | 1.1 | 0.0029 | 23452 | M. musculus early B-cell factor associated zinc finger transcription factor (Ebfaz) mRNA, complete cds | 3 | 10 | 8 | 1.00 | ||
| CACTATCTCC | 0 | 2 | 2 | 0.55 | 0.0015 | 29525 | ESTs, weakly similar to T33754 O/E-1-associated zinc finger protein Roaz-rat (Rattus norvegicus) | 9 | 28 | 8 | 0.57 | ||
| GTGGGATGGA | 1 | 1 | 2 | 0.55 | 0.0015 | 129369 | ESTs, weakly cimilar to I48208 zinc finger protein 30-mouse (M. musculus) | 4 | 5 | 2 | 1.00 | ||
| AAATAAATCT | 0 | 2 | 2 | 0.55 | 0.0015 | 31016 | ESTs, weakly similar to Z33A_HUMAN ZINC FINGER PROTEIN 33A (H. sapiens) | 5 | 5 | 1 | 1.00 | ||
| CCCATAAAAG | 1 | 0 | 1 | 0.27 | 0.00073 | 30405 | Zinc finger protein 94 | 5 | 12 | 6 | 0.83 | ||
| AAAGTACACA | 1 | 0 | 1 | 0.27 | 0.00073 | 102799 | ESTs, weakly similar to zinc finger protein (M. musculus) | 1 | 1 | 1 | 1.00 | ||
| TTTAAGTTAA | 1 | 0 | 1 | 0.27 | 0.00073 | 21914 | ESTs, highly similar to ZINC FINGER PROTEIN 91 (H. sapiens) | 6 | 26 | 13 | 0.69 | ||
| GTACGTTTCT | 1 | 0 | 1 | 0.27 | 0.00073 | 155690 | M. musculus zinc finger protein Sp5 mRNA, complete cds | 2 | 2 | 1 | 1.00 | ||
| GTCCCTCTCT | 1 | 0 | 1 | 0.27 | 0.00073 | 41364 | ESTs, weakly similar to zinc finger protein s11-6 (M. musculus) | 7 | 13 | 4 | 0.77 | ||
| GTTCATACAA | 1 | 0 | 1 | 0.27 | 0.00073 | 132523 | ESTs, weakly similar to ZF90_MOUSE ZINC FINGER PROTEIN 90 (M. musculus) | 1 | 3 | 2 | 0.67 | ||
| AGACATCACA | 0 | 1 | 1 | 0.27 | 0.00073 | 20430 | zinc finger protein 105 | 5 | 7 | 3 | 1.00 | ||
| AGTCACCAAT | 0 | 1 | 1 | 0.27 | 0.00073 | 2927 | zinc finger protein 30 | 2 | 5 | 4 | 1.00 | ||
| CTTTCTGTTC | 0 | 1 | 1 | 0.27 | 0.00073 | 30405 | zinc finger protein 94 | 3 | 12 | 6 | 0.67 | ||
| CATTCCACAT | 0 | 1 | 1 | 0.27 | 0.00073 | 12891 | zinc finger protein 326 | 3 | 6 | 4 | 1.00 | ||
| GCGCACTCAG | 1 | 0 | 1 | 0.27 | 0.00073 | 24775 | ESTs, weakly similar to zinc finger protein 64 (M. musculus) | 4 | 8 | 5 | 1.00 | ||
| CTCACAAATC | 0 | 1 | 1 | 0.27 | 0.00073 | 117547 | ESTs, highly similar to zinc finger transcription factor REST protein (R. norvegicus) | 1 | 1 | 1 | 1.00 | ||
| AGAAGGTGGT | 0 | 1 | 1 | 0.27 | 0.00073 | 12930 | BcL6-associated zinc finger protein | 2 | 2 | 1 | 1.00 | ||
| LIM containing | |||||||||||||
| GCCTGTGTAA | 10 | 13 | 23 | 6.3 | 0.017 | 21830 | reversion induced LIM gene | 28 | 34 | 4 | 0.91 | ||
| CACTTTTGCA | 2 | 4 | 6 | 1.6 | 0.0044 | 79380 | LIM homeobox protein 9 | 2 | 3 | 2 | 1.00 | ||
| TAAAGACACA | 1 | 1 | 2 | 0.55 | 0.0015 | 25785 | LIM domain binding 3 | 11 | 25 | 8 | 0.72 | ||
| GGATTTTACT | 0 | 1 | 1 | 0.27 | 0.00073 | 42242 | ISL1 transcription factor, LIM/homeodomain, (islet-1) | 3 | 6 | 2 | 0.67 | ||
| TATAGAGGAA | 0 | 1 | 1 | 0.27 | 0.00073 | 25785 | LIM domain binding 3 | 6 | 25 | 8 | 0.52 | ||
| ATCTCAGAAA | 0 | 1 | 1 | 0.27 | 0.00073 | 70551 | ESTs, weakly similar to LIM homeobox protein 9 (M. musculus) | 5 | 6 | 2 | 1.00 | ||
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Of the 264 FGFs, transcription factors, related genes, and homologous ESTs identified in our limb SAGE libraries with the ehm-tag-mapping method, only 43 tags, listed here, were specific to the limb sibraries after a virtual subtraction of the non-limb pooled SAGE library.
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↵Copies per cell was calculated assuming, on average, 500,000 transcripts in a cell (Hastie and Bishop 1976).
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↵See Methods for a description of these values.
