| {"id": "train:edit:Mic:DRAM1:chr12_101871113_101871613:3435", "task_type": "enhancer_editing", "split": "train", "messages": [{"role": "system", "content": "You are a genomics assistant for multimodal regulatory-sequence reasoning. Read structured metadata, promoter DNA, and enhancer DNA together. Use the provided cellular context and TF program. Return concise biological reasoning inside <reasoning_start> and <reasoning_end>. When DNA generation or editing is requested, return the final enhancer sequence inside <enhancer_dna_start> and <enhancer_dna_end>."}, {"role": "user", "content": "<task_start>cell_type_metadata_conditioned_enhancer_editing<task_end>\nEdit the reference enhancer under the provided objective.\nKeep the sequence within the edit budget and return the edited enhancer.\n<metadata_start>\ncell_type=Mic\ngene_name=DRAM1\npeak_name=chr12_101871113_101871613\n<expression_embedding_ref>Mic</expression_embedding_ref>\n<expression_vector_ref>Mic</expression_vector_ref>\n<metadata_end>\n<metadata_start>\nsource_cell_type=Mic\ntarget_cell_type=Ex\nsource_gene=DRAM1\ntarget_gene=DRAM1\nedit_type=cell_type_transfer\nedit_budget_bp=10\ntarget_tf=TBR1\ntarget_motif=AGGTGTGA\ninstruction=Shift the enhancer toward stronger compatibility with Ex while keeping the sequence close to the reference.\n<metadata_end>\n<promoter_dna_start>CTGGAGGGGAGTTTTTTTTGTTTTTTTTTTGTTTGTTTGTTTTTTGAGACAAGGTCTTGCTCTGTCACCCAGGCCGAGTGAAGTGGTGTGATAAAGGCTCACTGCAGCCTCGACCCCCAAGGCTCAAGTGATCATCCCAACTCAGTCTCCCGAGTAACTGGAACCGGCTTTTTTTCTTTTTCATTTTTTTTTTTTTTTTTTGTAGAAGAGGGGTTTCGCTATGTTACCCAGGCTGATCTCTAGTTCTTGGGTTCAAGCGATCCTCCCAACTCGGCCTCCCAAAGTGGTGGCATTCCAGGGGTGATGGCTTTTGGATGCCTCCCAAAGTGATGGCTATTCACGGCGCCCGGCCTGGGAAATCTTATTTCCAGGAAATATTCTCCAGTTGCGCTCTCCTGGAAAGCAGCACAATGGGCCTCCCGGCTCCGTGGGCGCGCAGTCCCACCCGCCTGCCCCGCACCCCACCCGCGTACTCTCCACCCCACCCGTTCCCACCCTGTCTGGGTTTTCGGGTGTTCACCATTGAGGTGGGAGCCACATCTGCGCCCCGTGACCTGGCGAACCTCATTGAACACTTCTGCCCGACCCCCGCAGCAGCAGCGCGACCGGATGGCATGGGTGTCACCACGCGGTGGCCACTCTCACTGCTGCGAAGCGCCGGCGGCGGGACCTCGGAGGGGGCGCCCTCGGGGTGCGAGGCCCGGCACTCCGGAAATCCCCCGGGAGGGAGGGGTTGGGAGAAATAAATCCTTTTCTCCAGAGTTGCGCAAGAGCCAGCGCGGTAGGGCCAGAGTGGGAAGGCCAGAGCGGGCGTCCCCGCCAGTGACCCCACGCCGCCCGTCCGCGCCCAACCCGGCCTCCGCCGAGTGTCCAAACCAAAAGCGAAAGGAACCCGACCCCGCGTCCCCTCCGGCGGCTCCGTAGTCGCGTCCGCTTGGAGCTCGCCGGGCGCCTCCGACCCTGCCGGGCCGCTTTGTGACTTCACTCGTTTCGCAACAAGCCCGGGCAGCCCGCGCCCCACCCA</promoter_dna_end>\n<reference_enhancer_start>AACCACCACCCTAAGTCAGCAGCTATCAACATCAAGGAAAACACTCCAACAGCAAAAAGGTTATGACTTGCTGAAGGCTCAGATGATGATTAGCAATGTTTTGCAATAAAGTATTTTTAAAAATACATATTTATCTTTTTTTTTTTTTCCCCGTAGAGATGAAGACCTCACTATGTTGCCCAGGCTGGTCTTGAACTCCTGGCCTCAAGCCATACTTCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCATGCCCTGCCACCAATAAAAGTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTCGCCCAGGCTAGAGTGCAGTGGTGCAATCTTGGCTTACTGCAACCTCTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTATAGGCGCCCGCCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTTATCATATTGGCCAGGCTG</reference_enhancer_end>\n<tool_context_start>Cell context is Mic with target gene DRAM1. The promoter is 1024 bp with GC 0.611. Expression context places the gene at rank 7503 in Mic with percentile 0.569. Per-cell-type expression for DRAM1 is dominant in End at 0.316; profile Ex=0.054, In=0.150, OPC=0.156, Ast=0.211, Oli=0.057, Mic=0.066, End=0.316. Top 128 Mic genes by expression: MALAT1 (1264.10), PLXDC2 (172.50), NEAT1 (135.12), LRMDA (89.02), DOCK4 (86.47), FRMD4A (76.14), SPP1 (73.30), MEF2C (50.13), FMNL2 (44.49), MEF2A (40.94), QKI (40.72), MAML2 (39.67), CHST11 (39.57), ARHGAP24 (38.11), ITPR2 (36.95), SLC8A1 (34.52), ARHGAP26 (34.31), TCF12 (32.98), DOCK8 (32.70), FOXN3 (31.90), LDLRAD4 (31.86), KCNQ3 (30.89), SLC11A1 (30.47), SLC9A9 (29.02), SLC1A3 (28.78), APBB1IP (28.35), ST6GAL1 (28.22), CELF2 (27.41), NAV3 (26.74), GNAQ (25.85), FCHSD2 (24.55), SAT1 (24.41), PTPRJ (24.14), FTL (23.84), PICALM (23.50), EPB41L2 (23.13), SRGAP2 (22.56), BMP2K (22.18), ZEB2 (22.13), RUNX1 (21.17), PRKCA (20.76), UBE2E2 (20.72), FTX (20.06), MTSS1 (19.79), ADAM28 (19.63), RNASET2 (19.50), DLEU1 (19.30), DISC1 (17.75), MAML3 (17.55), MED13L (17.55), ABR (17.40), CYFIP1 (17.07), SSH2 (16.94), ELMO1 (16.75), FAM49B (16.45), ZSWIM6 (16.11), RERE (15.80), SFMBT2 (15.68), ATP8B4 (15.61), AUTS2 (15.27), SH3RF3 (15.10), GRB2 (15.06), FYB1 (15.06), SDK1 (14.85), HDAC9 (14.53), RBM47 (13.81), MGAT4A (13.80), LYN (13.70), SMYD3 (13.66), JAZF1 (13.42), ZFAND3 (13.35), DDX5 (13.14), MERTK (13.10), TBC1D22A (13.09), CTSB (12.65), SBF2 (12.47), KCNMA1 (12.32), ETV6 (12.27), NPL (12.22), MARCH1 (12.06), RABGAP1L (12.00), NCK2 (12.00), DISP1 (11.99), JMJD1C (11.82), DENND3 (11.80), LNCAROD (11.73), GAB2 (11.70), TBC1D5 (11.63), FGD4 (11.40), EIF4G3 (11.33), LPP (11.29), ZFHX3 (11.24), MBNL1 (11.06), CHD9 (11.02), INPP5D (10.87), ATXN1 (10.84), SLCO2B1 (10.83), TRIO (10.67), TGFBR1 (10.65), MACF1 (10.60), ZBTB20 (10.53), WSB1 (10.47), AOAH (10.46), ARL15 (10.45), HIF1A (10.30), SORL1 (10.20), AKAP13 (10.19), APOE (10.11), AAK1 (10.04), TBXAS1 (10.04), MKLN1 (10.01), DIP2B (9.82), MAP4K4 (9.79), ST6GALNAC3 (9.58), SAMSN1 (9.57), ANKS1A (9.55), PTPRE (9.55), MBD5 (9.51), DIAPH2 (9.44), EXOC4 (9.40), BACH1 (9.31), MKNK1 (9.29), TNRC6B (9.19), NF1 (9.15), ATG7 (9.15), IPCEF1 (9.14), DDX17 (9.09), PIAS1 (8.94). Evolution proxy score is 0.697 with expression stability 0.618 (expression_stability_proxy_v1 over the 7-cell-type expression table). Promoter motif scan reports TATA hits=0, Inr hits=8, DPE hits=0, promoter_likeness_score=1.000. Sequence quality for the promoter reports quality_score=0.903, GC=0.448, repeat_fraction=0.321, kmer_entropy_norm=0.944. Peak coordinates parsed to chr12:101871113-101871613 (500 bp, midpoint 101871363). Reviewed TF program for Mic includes SPI1, IRF8. TFBS scan via fimo found 74 distinct TFs (132 total hits); top binders: MEF2C(hits=2, strength=8.95, best=13.10, Mic_expr=50.13, strands=+|-, pos=[457-467-@13.10[CTAAAAATACA]; 117-127+@10.75[TTAAAAATACA]]); MEF2A(hits=3, strength=12.74, best=13.11, Mic_expr=40.94, strands=+|-, pos=[458-467-@13.11[CTAAAAATAC]; 111-120-@10.54[TTAAAAATAC]; 117-126+@10.54[TTAAAAATAC]]); Nfat5(hits=1, strength=4.21, best=11.07, Mic_expr=3.03, strands=+, pos=[34-41+@11.07[AAGGAAAA]]); NFIC(hits=6, strength=29.54, best=12.35, Mic_expr=1.88, strands=+|-, pos=[200-213+@12.22[TGGCCTCAAGCCAT]; 199-213-@12.35[ATGGCTTGAGGCCAG]; 199-213+@11.53[CTGGCCTCAAGCCAT]]); STAT1(hits=1, strength=4.33, best=10.71, Mic_expr=1.71, strands=+, pos=[282-294+@10.71[AGTTTTTTTTTTT]]); Plagl1(hits=1, strength=4.25, best=11.52, Mic_expr=1.50, strands=-, pos=[200-207-@11.52[TGAGGCCA]]); NR6A1(hits=1, strength=4.20, best=10.16, Mic_expr=1.24, strands=-, pos=[186-199-@10.16[GGAGTTCAAGACCA]]); KLF7(hits=1, strength=4.03, best=10.97, Mic_expr=0.75, strands=-, pos=[4-11-@10.97[GGGTGGTG]]); KLF3(hits=1, strength=4.06, best=9.62, Mic_expr=0.70, strands=+, pos=[259-268+@9.62[CACCATGCCC]]); Mafb(hits=1, strength=4.27, best=11.65, Mic_expr=0.64, strands=-, pos=[15-25-@11.65[TAGCTGCTGAC]]). aggregate_tfbs_score=1.000 Additional 64 TFs with motif hits: NFIB(3), FOSL2(1), ZNF143(1), ZNF136(1), ZNF76(1), MEF2D(1), ATF4(1), ZNF140(1), CEBPG(1), MAFK(2), Mafg(2), ZNF257(2), Vdr(1), TFAP4(1), ZNF528(1), ZNF85(1), ZNF213(3), Nr2F6(1), TCF7L1(1), MAFF(1), CEBPA(2), ZNF460(3), NFIX(2), RARA(1), MEF2B(1), ZNF558(1), ESR2(1), ZNF135(4), ZNF384(20), Rarb(1), KLF4(1), Hmga1(3), ZNF324(1), RXRB(2), ZNF574(1), ZNF770(3), Rarg(1), ZKSCAN3(2), ZNF524(1), ZBTB7C(1), TFAP2C(3), NRL(1), FEZF2(5), THAP1(1), ZNF416(1), Hoxa13(2), Zfp809(2), TFAP2B(2), TFAP2A(2), Hoxd13(2), HOXB13(1), NR5A1(1), CDX2(1), Gfi1B(1), Zfp961(1), FOXE1(1), CDX4(1), OTX2(1), HOXD9(1), CDX1(1), Prdm14(1), MAFA(1), HOXA10(1), E2F8(1). Expressed TFs in Mic with binding sites in the scanned sequence: MEF2C(50.13), MEF2A(40.94), Nfat5(3.03), NFIC(1.88), STAT1(1.71), Plagl1(1.50), NR6A1(1.24), KLF7(0.75), KLF3(0.70), Mafb(0.64), NFIB(0.37), FOSL2(0.37), ZNF143(0.33), ZNF136(0.28), ZNF76(0.25), MEF2D(0.24), ATF4(0.22), ZNF140(0.19), CEBPG(0.17), MAFK(0.15). Sliding GC/CpG profile reports mean_gc=0.443, mean_cpg_oe=n/a. Requested edit type is cell_type_transfer with budget 10. Target TF prior is TBR1 using motif AGGTGTGA. Reference enhancer GC is 0.448; plan the edit on this reference so the motif insertion preserves the surrounding TF program. Motif edit plan places the target at reference position 248, requiring 2 substitutions (edit_budget=10, within_budget=true).</tool_context_end>"}, {"role": "assistant", "content": "<reasoning_start>Reference context is Mic for gene DRAM1. Requested edit type is cell_type_transfer with budget 10. Performed 2 substitutions while keeping sequence length fixed.</reasoning_end>\n<enhancer_dna_start>AAACACCACCCTAAGTCAGCAGCTATCAACATCAAGGAAAACACTCCAACAGCAAAAAGGTTATGACTTGCTGAAGGCTCAGATGATGATTAGCAATGTTTTGCAATAAAGTATTTTTAAAAATACATATTTATCTTTTTTTTTTTTTCCCCGTAGAGATGAAGACCTCACTATGTTGCCCAGGCTGGTCTTGAACTCCTGGCCTCAAGCCATACTTCTGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCATGCCCTGCCACCAATAAAAGTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTTGCTCTGTCGCCCAGGCTAGAGTGCAGTGGTGCAATCTTGGCTTACTGCAACCTCTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTATAGGCGCCCGCCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTTATCATATTGGCCAGGCTG</enhancer_dna_end>"}], "metadata": {"cell_type": "Mic", "gene_name": "DRAM1", "peak_name": "chr12_101871113_101871613", "source_relpath": "Mic/23.csv", "source_row_index": 3435, "split_name": "separatedQA", "reasoning_richness": "raw", "tf_scan_backend": "exact", "tf_edit_backend": "exact", "expression_embedding_key": "Mic", "expression_vector_key": "Mic", "edit_type": "cell_type_transfer", "edit_budget": 10, "target_cell_type": "Ex", "target_gene": "DRAM1", "target_tf": "TBR1", "target_motif": "AGGTGTGA", "oracle_expected_edit_cost": 2, "oracle_target_tf_present": true, "oracle_source_tf_hits_after_edit": [], "rft_source": "candidate"}} |
| {"id": "train:edit:Mic:ZNF599:chr19_34985433_34985933:2249", "task_type": "enhancer_editing", "split": "train", "messages": [{"role": "system", "content": "You are a genomics assistant for multimodal regulatory-sequence reasoning. Read structured metadata, promoter DNA, and enhancer DNA together. Use the provided cellular context and TF program. Return concise biological reasoning inside <reasoning_start> and <reasoning_end>. When DNA generation or editing is requested, return the final enhancer sequence inside <enhancer_dna_start> and <enhancer_dna_end>."}, {"role": "user", "content": "<task_start>cell_type_metadata_conditioned_enhancer_editing<task_end>\nEdit the reference enhancer under the provided objective.\nKeep the sequence within the edit budget and return the edited enhancer.\n<metadata_start>\ncell_type=Mic\ngene_name=ZNF599\npeak_name=chr19_34985433_34985933\n<expression_embedding_ref>Mic</expression_embedding_ref>\n<expression_vector_ref>Mic</expression_vector_ref>\n<metadata_end>\n<metadata_start>\nsource_cell_type=Mic\ntarget_cell_type=Mic\nsource_gene=ZNF599\ntarget_gene=QSER1\nedit_type=promoter_retarget\nedit_budget_bp=10\ntarget_tf=RUNX1\ntarget_motif=TGTGGT\ninstruction=Retarget the enhancer toward promoter compatibility for gene QSER1 in Mic.\n<metadata_end>\n<promoter_dna_start>GCCGCTACGGGAACGCCCCTCTGCGCCTTCCGTCTATGGCTTGGGGTCGGCTTCCGTCCCTTGTAGCACTGCCTTCTGGGTAATGTAGTTTGACGGAATCCGGGTGGTACCTGGAGCGCACTTTCTGTTCTCGGTGAGGCGGCTTCTCAAGGCTCCCAAGAAAGGGATTGGCTTCACCTCTTCTTAAAGGAGAGGCACACAGAGTTCCGTGGAAATTATCTGAGGCAATGACCCACTCTCAAATGTCTCTACCAGGCAACTCACGCCTTGACTTTCCTCCCTGTGTATCCCTGCGCCAGCAGTTCATCTCTCTGAGCCTTGAGATGGAGATTCCTAAGGAAAATGAAGATAATTATTTAATATGATAATATTAAAATTTCCCCTATCAGTAATTTTCAGATGACATCAGCATTACCTGCGAATTTGTTACCAATGCAAGTTCTTAGTCCCCACCCACTGAATCAGGTACTCTGGGGGGTGGGACCCAGCCCTCTGCTTAACTTGTCCAGGAAAAGTGGATGCTGCAAAACATTTGAGAACCAGACTCTTTAAATTCCAGTAAATAAATGAGACAAAGCCACCTGTTTGGTGGGAAGTAACTAAGAATTGCTTAGCACTGGGCCTGGAACATACCGATAAGAACATAAGAGCTATTGCTGTCATTATTAATATTCTGTATTATTGGCAACATCATCACAATACACTGCTAGGGGAGGGTCTGAGATACTTCTTTGCAGACTCTGATATTTGTCAAAACAAATACGTTGACTGATTCAACAGGAGCCTCATGAATACTGTTTAAATTTTACATAATAATACGTTGCAGCATTTGGCGTATGCATCTTTTTAAAACGGTATATGCAGGAGGGTTTCCTAATATACAGGTAGACCTATTGCCCAAGGGATACTTTCTTACATGATTCAAAACTTAGGATCACTGAGACTAATTACCTGCAGCCCTAAGGGAAGAGTGGAGTTGACATGGTTTCTAGTTTGTGATGTAAGATGGCGTGTCACTGTTCAT</promoter_dna_end>\n<reference_enhancer_start>CCACCCCTAAATCTGCCGGTTATGCATTTCTCTTTTAGCTACCTTTGACTTGGGGGGAACTCTTCCTGTGCCAAGTAATTGAAGACATTTGTGCACAGTAGGGGGAAGCTTTTGTTTCTGCCTAGCAGGAAGCATTTCCAGTTTCCAGGAACGTTGCTAATTTAGAGGAATATGTGTATGTGTGAGTTGCTTAAACTTCCTTTGCCCCAGATGGCCAAGAACAGCATCCGGAAAGCCACTTACAGTGCAGCAGCTCAGCCCCACCTCCTCCTGGCAAGCAGGCAGCATCCTGTCCAGACAACTGTGTGTTGATCCCTCCTCCAGCACTGCTTTCCTGGCCCCAGACATCAATGGCAGCAAGTGCCAGGAAGGTTCCAACGGCCAGGCTGTATCTCTCACTCTTTGTGTTCCAAACAGGTGACTGCTGGTTTGCCCATCACAACGAGCCTCTTGTGCCTTGTAGGCTTAGTCTAAGATCAGAACCATGGGCACTCCTTCTT</reference_enhancer_end>\n<tool_context_start>Cell context is Mic with target gene ZNF599. The promoter is 1024 bp with GC 0.440. Expression context places the gene at rank 11837 in Mic with percentile 0.320. Per-cell-type expression for ZNF599 is dominant in OPC at 0.050; profile Ex=0.020, In=0.030, OPC=0.050, Ast=0.011, Oli=0.017, Mic=0.005, End=0.015. Top 128 Mic genes by expression: MALAT1 (1264.10), PLXDC2 (172.50), NEAT1 (135.12), LRMDA (89.02), DOCK4 (86.47), FRMD4A (76.14), SPP1 (73.30), MEF2C (50.13), FMNL2 (44.49), MEF2A (40.94), QKI (40.72), MAML2 (39.67), CHST11 (39.57), ARHGAP24 (38.11), ITPR2 (36.95), SLC8A1 (34.52), ARHGAP26 (34.31), TCF12 (32.98), DOCK8 (32.70), FOXN3 (31.90), LDLRAD4 (31.86), KCNQ3 (30.89), SLC11A1 (30.47), SLC9A9 (29.02), SLC1A3 (28.78), APBB1IP (28.35), ST6GAL1 (28.22), CELF2 (27.41), NAV3 (26.74), GNAQ (25.85), FCHSD2 (24.55), SAT1 (24.41), PTPRJ (24.14), FTL (23.84), PICALM (23.50), EPB41L2 (23.13), SRGAP2 (22.56), BMP2K (22.18), ZEB2 (22.13), RUNX1 (21.17), PRKCA (20.76), UBE2E2 (20.72), FTX (20.06), MTSS1 (19.79), ADAM28 (19.63), RNASET2 (19.50), DLEU1 (19.30), DISC1 (17.75), MAML3 (17.55), MED13L (17.55), ABR (17.40), CYFIP1 (17.07), SSH2 (16.94), ELMO1 (16.75), FAM49B (16.45), ZSWIM6 (16.11), RERE (15.80), SFMBT2 (15.68), ATP8B4 (15.61), AUTS2 (15.27), SH3RF3 (15.10), GRB2 (15.06), FYB1 (15.06), SDK1 (14.85), HDAC9 (14.53), RBM47 (13.81), MGAT4A (13.80), LYN (13.70), SMYD3 (13.66), JAZF1 (13.42), ZFAND3 (13.35), DDX5 (13.14), MERTK (13.10), TBC1D22A (13.09), CTSB (12.65), SBF2 (12.47), KCNMA1 (12.32), ETV6 (12.27), NPL (12.22), MARCH1 (12.06), RABGAP1L (12.00), NCK2 (12.00), DISP1 (11.99), JMJD1C (11.82), DENND3 (11.80), LNCAROD (11.73), GAB2 (11.70), TBC1D5 (11.63), FGD4 (11.40), EIF4G3 (11.33), LPP (11.29), ZFHX3 (11.24), MBNL1 (11.06), CHD9 (11.02), INPP5D (10.87), ATXN1 (10.84), SLCO2B1 (10.83), TRIO (10.67), TGFBR1 (10.65), MACF1 (10.60), ZBTB20 (10.53), WSB1 (10.47), AOAH (10.46), ARL15 (10.45), HIF1A (10.30), SORL1 (10.20), AKAP13 (10.19), APOE (10.11), AAK1 (10.04), TBXAS1 (10.04), MKLN1 (10.01), DIP2B (9.82), MAP4K4 (9.79), ST6GALNAC3 (9.58), SAMSN1 (9.57), ANKS1A (9.55), PTPRE (9.55), MBD5 (9.51), DIAPH2 (9.44), EXOC4 (9.40), BACH1 (9.31), MKNK1 (9.29), TNRC6B (9.19), NF1 (9.15), ATG7 (9.15), IPCEF1 (9.14), DDX17 (9.09), PIAS1 (8.94). Evolution proxy score is 0.437 with expression stability 0.609 (expression_stability_proxy_v1 over the 7-cell-type expression table). Promoter motif scan reports TATA hits=0, Inr hits=4, DPE hits=0, promoter_likeness_score=0.800. Sequence quality for the promoter reports quality_score=0.929, GC=0.504, repeat_fraction=0.291, kmer_entropy_norm=0.949. Peak coordinates parsed to chr19:34985433-34985933 (500 bp, midpoint 34985683). Reviewed TF program for Mic includes SPI1, IRF8. TFBS scan via fimo found 97 distinct TFs (145 total hits); top binders: FLI1(hits=3, strength=12.64, best=11.15, Mic_expr=6.87, strands=+|-, pos=[125-138+@11.15[GCAGGAAGCATTTC]; 219-232-@10.71[TCCGGATGCTGTTC]; 286-296-@10.85[TGGACAGGATG]]); IKZF1(hits=2, strength=8.58, best=11.81, Mic_expr=4.96, strands=+|-, pos=[63-70-@11.81[CACAGGAA]; 124-131+@11.37[AGCAGGAA]]); PPARD(hits=1, strength=4.01, best=5.06, Mic_expr=3.89, strands=-, pos=[39-52-@5.06[CAAGTCAAAGGTAG]]); ELF1(hits=2, strength=8.65, best=12.82, Mic_expr=2.14, strands=+|-, pos=[60-68-@12.82[CAGGAAGAG]; 355-363+@10.06[CAGCAAGTG]]); SMAD3(hits=2, strength=9.06, best=11.69, Mic_expr=2.08, strands=+|-, pos=[291-300+@11.69[TGTCCAGACA]; 291-300-@10.64[TGTCTGGACA]]); STAT3(hits=3, strength=13.40, best=13.65, Mic_expr=2.03, strands=+|-, pos=[143-151-@13.65[TTCCTGGAA]; 143-151+@12.84[TTCCAGGAA]; 362-370+@11.76[TGCCAGGAA]]); NFIC(hits=5, strength=21.79, best=13.37, Mic_expr=1.88, strands=+|-, pos=[271-285-@8.85[CTGCCTGCTTGCCAG]; 271-285+@8.05[CTGGCAAGCAGGCAG]; 69-75-@13.37[CTTGGCA]]); REL(hits=1, strength=4.10, best=10.98, Mic_expr=1.76, strands=-, pos=[230-239-@10.98[GTGGCTTTCC]]); BCL6(hits=1, strength=4.35, best=10.58, Mic_expr=1.76, strands=+, pos=[140-152+@10.58[AGTTTCCAGGAAC]]); STAT1(hits=3, strength=13.94, best=15.62, Mic_expr=1.71, strands=+|-, pos=[143-151+@15.62[TTCCAGGAA]; 143-151-@12.84[TTCCTGGAA]; 362-370+@10.91[TGCCAGGAA]]). aggregate_tfbs_score=1.000 Additional 87 TFs with motif hits: Stat2(2), ZKSCAN1(1), Plagl1(1), ETV5(1), ETS2(2), RFX7(1), PLAG1(1), Spi1(2), SP3(1), FOXO1(1), SREBF2(1), Stat5b(2), SREBF1(1), PPARA(1), ZNF449(1), Stat5a(4), CTCF(3), ZNF680(1), Prdm4(1), SMAD5(2), NFIB(2), ERF(2), PATZ1(1), Erg(3), ZNF708(1), GABPA(2), REST(1), ZNF175(3), SP2(1), ZNF140(1), RELA(1), ZNF682(1), ZNF701(1), ZNF549(1), ZBTB7A(1), ZNF257(1), ETV1(4), ZNF528(1), FOXJ2(1), ZNF213(1), ZKSCAN5(1), Sox1(1), Sox7(1), ZNF189(1), ZNF341(1), Irf1(2), ZNF460(1), ZNF281(3), RARA(2), ZNF558(1), ZIC1(1), Stat4(3), KLF16(1), ZNF677(1), KLF4(1), ZIC4(1), RXRB(1), Zic2(1), ETV2(4), Neurod2(1), TWIST1(1), Nkx3-1(1), SOX9(1), SCRT1(1), KLF5(1), TFAP2C(2), HES7(1), NEUROD1(1), ZNF669(1), Ikzf3(3), INSM1(1), SNAI2(1), ELF3(2), EHF(2), TFAP2B(2), Elf5(1), RORC(1), Wt1(1), NEUROG2(1), Atoh1(1), MYOD1(1), Nkx3-2(1), Ptf1A(1), ZIM3(1), SNAI1(1), Zfp335(1), Rfx6(1). Expressed TFs in Mic with binding sites in the scanned sequence: FLI1(6.87), IKZF1(4.96), PPARD(3.89), ELF1(2.14), SMAD3(2.08), STAT3(2.03), NFIC(1.88), REL(1.76), BCL6(1.76), STAT1(1.71), Stat2(1.70), ZKSCAN1(1.50), Plagl1(1.50), ETV5(1.46), ETS2(1.44), RFX7(1.37), PLAG1(1.15), Spi1(1.13), SP3(1.04), FOXO1(1.00). Sliding GC/CpG profile reports mean_gc=0.503, mean_cpg_oe=n/a. Requested edit type is promoter_retarget with budget 10. Target TF prior is RUNX1 using motif TGTGGT. Reference enhancer GC is 0.504; plan the edit on this reference so the motif insertion preserves the surrounding TF program. Motif edit plan places the target at reference position 304, requiring 1 substitutions (edit_budget=10, within_budget=true).</tool_context_end>"}, {"role": "assistant", "content": "<reasoning_start>Reference context is Mic for gene ZNF599. Requested edit type is promoter_retarget with budget 10. Performed 1 substitutions while keeping sequence length fixed.</reasoning_end>\n<enhancer_dna_start>AAACCCCTAAATCTGCCGGTTATGCATTTCTCTTTTAGCTACCTTTGACTTGGGGGGAACTCTTCCTGTGCCAAGTAATTGAAGACATTTGTGCACAGTAGGGGGAAGCTTTTGTTTCTGCCTAGCAGGAAGCATTTCCAGTTTCCAGGAACGTTGCTAATTTAGAGGAATATGTGTATGTGTGAGTTGCTTAAACTTCCTTTGCCCCAGATGGCCAAGAACAGCATCCGGAAAGCCACTTACAGTGCAGCAGCTCAGCCCCACCTCCTCCTGGCAAGCAGGCAGCATCCTGTCCAGACAACTGTGTGGTGATCCCTCCTCCAGCACTGCTTTCCTGGCCCCAGACATCAATGGCAGCAAGTGCCAGGAAGGTTCCAACGGCCAGGCTGTATCTCTCACTCTTTGTGTTCCAAACAGGTGACTGCTGGTTTGCCCATCACAACGAGCCTCTTGTGCCTTGTAGGCTTAGTCTAAGATCAGAACCATGGGCACTCCTTCTT</enhancer_dna_end>"}], "metadata": {"cell_type": "Mic", "gene_name": "ZNF599", "peak_name": "chr19_34985433_34985933", "source_relpath": "Mic/50.csv", "source_row_index": 2249, "split_name": "separatedQA", "reasoning_richness": "raw", "tf_scan_backend": "exact", "tf_edit_backend": "exact", "expression_embedding_key": "Mic", "expression_vector_key": "Mic", "edit_type": "promoter_retarget", "edit_budget": 10, "target_cell_type": "Mic", "target_gene": "QSER1", "target_tf": "RUNX1", "target_motif": "TGTGGT", "oracle_expected_edit_cost": 1, "oracle_target_tf_present": true, "oracle_source_tf_hits_after_edit": ["RUNX1"], "rft_source": "candidate"}} |
