{"text_format":"2","workbook":"xlsx","n_sheets":5,"sheets":["README","Gene Set for Simple Weighting S","Gene Set for Complex Weighting ","GSCA Results for Simple Weighti","GSCA Results for Complex Weight"],"not_rendered":{"charts":0,"images":1,"macros":0,"external_links":0,"defined_names":0,"comments":0,"pivot_tables":0},"unopened":[],"bounds":{"document_bytes":16777216,"sheet_cells":100000,"run_cost":"one","rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0,"cell_chars":16384,"cell_head_chars":4096},"cells_cut":0,"cells_raw":0,"read":"whole","date_system":"1904"}

{"sheet":"README","index":0,"n_rows":4,"n_cols":1,"rows_kept":4,"cut":false,"hidden":false,"merged":[[0,0,0,2],[2,0,2,2],[3,0,3,2],[1,0,1,2]]}
["This xlsx file contains following four tables:"]
[]
["Gene Set for Simple/Complex Weighting Scheme: This table contains gene set of Shh target genes for simple/complex weighting schemes. The weights used in each weighting scheme are also shown. Both tables can be directly uploaded in GSCA."]
["GSCA Results for Simple/Complex Weighting Scheme: This table contains the output of GSCA analysis for gene sets with simple/complex weighting schemes. For complex weighting scheme, the contexts discussed in the supplementary materials (e.g. medulloblastoma) are highlighted with red."]

{"sheet":"Gene Set for Simple Weighting S","index":1,"n_rows":19,"n_cols":3,"rows_kept":19,"cut":false,"hidden":false,"merged":[]}
["Gene","Weight","Geneset"]
[18484,1,"Shh"]
[59012,1,"Shh"]
[14632,1,"Shh"]
[13386,1,"Shh"]
[20471,1,"Shh"]
[238257,1,"Shh"]
[71704,1,"Shh"]
[107587,1,"Shh"]
[108052,1,"Shh"]
[74152,1,"Shh"]
[19207,1,"Shh"]
[12319,1,"Shh"]
[12804,1,"Shh"]
[20423,1,"Shh"]
[494519,1,"Shh"]
[15111,1,"Shh"]
[15245,1,"Shh"]
[24046,1,"Shh"]

{"sheet":"Gene Set for Complex Weighting ","index":2,"n_rows":19,"n_cols":3,"rows_kept":19,"cut":false,"hidden":false,"merged":[]}
["Gene","Weight","Geneset"]
[18484,0.1257409,"Shh"]
[59012,0.018666,"Shh"]
[14632,0.9905948,"Shh"]
[13386,0.4585372,"Shh"]
[20471,0.1895407,"Shh"]
[238257,0.1999168,"Shh"]
[71704,0.329504,"Shh"]
[107587,0.1705499,"Shh"]
[108052,0.03104703,"Shh"]
[74152,0.144977,"Shh"]
[19207,1,"Shh"]
[12319,0.01207289,"Shh"]
[12804,0.1667054,"Shh"]
[20423,0.008978352,"Shh"]
[494519,0,"Shh"]
[15111,0.4479831,"Shh"]
[15245,0.06438499,"Shh"]
[24046,0.1951639,"Shh"]

{"sheet":"GSCA Results for Simple Weighti","index":3,"n_rows":14,"n_cols":7,"rows_kept":14,"cut":false,"hidden":false,"merged":[]}
["Rank","Active","Total","FoldChange","Adj.Pvalue","SampleType","ExperimentID"]
[1,112,165,3.707,8.81e-43,"liver:normal","GSE12712;GSE13149;GSE13583;GSE13585;GSE5128;GSE5959;GSE6297;GSE6632;GSE7357;GSE8292;GSE8316;GSE8396;GSE8295;GSE8969;GSE9892;GSE9954;GSE10246;GSE10493;GSE10744;GSE10895;GSE11632;GSE11899"]
[2,39,48,4.387,3.38e-18,"liver:na","GSE11923"]
[3,15,15,5.205,9.66e-09,"e105_craniofacial_tissue,_first_branchial_arch:we_will_separately_dissect_the_maxillary_and_mandibular_branches_of_the_e105_first_branchial_arch_from_wild_type,_dlx2,_dlx12_and_dlx56_mutants_the_tissues_wil_be_flash_frozen_within_1_min_of_removalwe_have_not_performed_the_dissections_yet_so_we_dont_know_how_much_rna_will_be_get_from_each_sample,_but_previous_experience_suggests_that_we_will_need_~10_branchial_archesexperiment;treatment,_type=nucleic_acid_extraction,_description=we_anticipate_using_this_method_as_it_was_recommended_by_tgen_for_small_amounts_of_tissue","GSE4774"]
[4,34,71,2.604,1.18e-05,"(spretei_x_fvbn)_x_fvbn_tail_epidermis:fvbbx","GSE12248"]
[5,10,10,5.078,5.01e-05,"fetal_liver:normal","GSE13044"]
[6,10,10,5.078,5.01e-05,"fetal_lung:normal","GSE13044"]
[7,10,10,5.078,5.01e-05,"neonatal_small_intestine:normal","GSE6065"]
[8,7,7,4.925,0.008410000000000001,"mandibular_prominence_tissue_e100:normal","GSE7759"]
[9,7,7,4.925,0.008410000000000001,"mandibular_prominence_tissue_e110:normal","GSE7759"]
[10,7,7,4.925,0.008410000000000001,"mandibular_prominence_tissue_e120:normal","GSE7759"]
[11,7,7,4.925,0.008410000000000001,"mandibular_prominence_tissue_e125:normal","GSE7759"]
[12,6,6,4.845,0.0463,"cervix:etoh_treated,_vehicle","GSE10392"]
[13,6,6,4.845,0.0463,"cervix:mpatreatment_for_48hrs","GSE10392"]

{"sheet":"GSCA Results for Complex Weight","index":4,"n_rows":29,"n_cols":7,"rows_kept":29,"cut":false,"hidden":false,"merged":[]}
["Rank","Active","Total","FoldChange","Adj.Pvalue","SampleType","ExperimentID"]
[1,21,21,6.812,1.43e-15,"cerebellum:primary_tumor_cells__isolated_from_conventional_patched_medulloblastomas","GSE12430"]
[2,15,15,6.708,2.01e-10,"e105_craniofacial_tissue,_first_branchial_arch:we_will_separately_dissect_the_maxillary_and_mandibular_branches_of_the_e105_first_branchial_arch_from_wild_type,_dlx2,_dlx12_and_dlx56_mutants_the_tissues_wil_be_flash_frozen_within_1_min_of_removalwe_have_not_performed_the_dissections_yet_so_we_dont_know_how_much_rna_will_be_get_from_each_sample,_but_previous_experience_suggests_that_we_will_need_~10_branchial_archesexperiment;treatment,_type=nucleic_acid_extraction,_description=we_anticipate_using_this_method_as_it_was_recommended_by_tgen_for_small_amounts_of_tissue","GSE4774"]
[3,12,13,6.148,8.42e-07,"retinal_progenitor_cell_p0:normal","GSE9811"]
[4,10,10,6.535,3.81e-06,"fetal_liver:normal","GSE13044"]
[5,10,10,6.535,3.81e-06,"fetal_lung:normal","GSE13044"]
[6,10,10,6.535,3.81e-06,"neonatal_small_intestine:normal","GSE6065"]
[7,10,11,5.991,3.66e-05,"retinal_progenitor_cell_e165:normal","GSE9811"]
[8,8,8,6.412,0.000195,"e14tg2a_cells:10_pg_amplified","GSE4308;GSE4309"]
[9,8,8,6.412,0.000195,"e14tg2a_cells:normal","GSE4308;GSE4309"]
[10,7,7,6.328,0.00139,"cerebellum:cerebellar_tumor_from_olig2tvacre:smom2_mice","GSE11859"]
[11,7,7,6.328,0.00139,"frontonasal_prominence_tissue_e110:normal","GSE7759"]
[12,7,7,6.328,0.00139,"frontonasal_prominence_tissue_e115:normal","GSE7759"]
[13,7,7,6.328,0.00139,"frontonasal_prominence_tissue_e120:normal","GSE7759"]
[14,7,7,6.328,0.00139,"frontonasal_prominence_tissue_e125:normal","GSE7759"]
[15,7,7,6.328,0.00139,"mandibular_prominence_tissue_e100:normal","GSE7759"]
[16,7,7,6.328,0.00139,"mandibular_prominence_tissue_e105:normal","GSE7759"]
[17,7,7,6.328,0.00139,"mandibular_prominence_tissue_e110:normal","GSE7759"]
[18,7,7,6.328,0.00139,"mandibular_prominence_tissue_e115:normal","GSE7759"]
[19,7,7,6.328,0.00139,"mandibular_prominence_tissue_e120:normal","GSE7759"]
[20,7,7,6.328,0.00139,"mandibular_prominence_tissue_e125:normal","GSE7759"]
[21,7,7,6.328,0.00139,"maxillary_prominence_tissue_e105:normal","GSE7759"]
[22,7,7,6.328,0.00139,"maxillary_prominence_tissue_e115:normal","GSE7759"]
[23,7,7,6.328,0.00139,"maxillary_prominence_tissue_e120:normal","GSE7759"]
[24,7,7,6.328,0.00139,"maxillary_prominence_tissue_e125:normal","GSE7759"]
[25,9,12,4.985,0.00401,"embryonic_stem_cells:r1,_undifferentiated_mouse_embryonic_stem_cells;_fractionated_polysomal_rna","GSE9563"]
[26,6,6,6.219,0.00991,"embryonic_head_tissue_e135:normal","GSE8091"]
[27,6,6,6.219,0.00991,"embryonic_head_tissue_e95:normal","GSE8091"]
[28,6,6,6.219,0.00991,"es_cells:ezh2null_es_cells_at_day_0_(undifferentiated)","GSE12982"]