{"text_format":"3","workbook":"xlsx","n_sheets":5,"sheets":["Supplementary Table 1","Supplementary Table 2","Supplementary Table3","Supplementary Table 4","Supplementary Table 5"],"read":"whole","date_system":"1900"}

{"sheet":"Supplementary Table 1","index":0,"n_rows":52,"n_cols":8,"rows_kept":52}
["Supplementary Table 1 Quality of the TCGA H&E slides as assessed by a specialist breast pathologist."]
["A five-level scoring was developed to indicate the quality associated with the H&E data from TCGA-BRCA data. "]
["Here, 1=uninterpretable, 2=poor staining/section quality compromising interpretation, 3=moderately poor stain/section quality, 4=good staining/section quality, and 5=excellent staining/section quality."]
[]
[]
["Index","Image file name","Score","Notes","Index","Image file name","Score","Notes"]
[1,"TCGA-3C-AALK",4,"Eosin too heavy",47,"TCGA-AO-A12D",4,"Haematoxylin heavy"]
[2,"TCGA-A1-A0SM",5,null,48,"TCGA-AO-A12G",3,"Understained/faded"]
[3,"TCGA-A1-A0SN",5,null,49,"TCGA-AQ-A04L",5]
[4,"TCGA-A2-A04X",4,"Haematoxylin too heavy",50,"TCGA-AQ-A0Y5",4,"Eosin too heavy"]
[5,"TCGA-A2-A0CX",4,"Haematoxylin too heavy",51,"TCGA-AR-A0TX",5,"Mostly DCIS, only focal invasive"]
[6,"TCGA-A2-A0EQ",4,"Eosin weak",52,"TCGA-AR-A1AT",4,"Slightly overstained"]
[7,"TCGA-A2-A0T1",4,"Haematoxylin weak",53,"TCGA-AR-A1AX",5]
[8,"TCGA-A2-A0YG",5,null,54,"TCGA-AR-A24U",5]
[9,"TCGA-A2-A3XZ",3,"Eosin too weak, haematoxylin too heavy",55,"TCGA-AR-A254",4,"Bit overstained"]
[10,"TCGA-A7-A2KD",3,"Haematoxylin very heavy",56,"TCGA-AR-A255",4,"Bit overstained"]
[11,"TCGA-A7-A4SF",4,"Haematoxylin too heavy",57,"TCGA-AR-A2LJ",4,"Bit overstained"]
[12,"TCGA-A8-A06T",4,"Eosin too weak",58,"TCGA-AR-A5QN",4,"Bit overstained"]
[13,"TCGA-A8-A076",4,"Eosin too heavy",59,"TCGA-BH-A0AW",2,"Overstained and underfixed"]
[14,"TCGA-A8-A07B",5,null,60,"TCGA-BH-A0B6",4,"Overstained"]
[15,"TCGA-A8-A07I",5,null,61,"TCGA-BH-A0HY",4,"Overstained"]
[16,"TCGA-A8-A07R",5,null,62,"TCGA-BH-A18H",3,"Haematoxylin very heavy, pure DCIS"]
[17,"TCGA-A8-A08B",5,null,63,"TCGA-BH-A18I",3,"Haematoxylin too heavy"]
[18,"TCGA-A8-A08C",5,null,64,"TCGA-BH-A18T",5]
[19,"TCGA-A8-A08G",5,null,65,"TCGA-BH-A42T",3,"Haematoxylin very heavy"]
[20,"TCGA-A8-A08P",4,"Haematoxylin too heavy",66,"TCGA-C8-A12Q",5]
[21,"TCGA-A8-A08S",5,null,67,"TCGA-C8-A1HF",5]
[22,"TCGA-A8-A08T",5,null,68,"TCGA-C8-A278",5]
[23,"TCGA-A8-A08X",5,null,69,"TCGA-C8-A3M8",3,"Haematoxylin very heavy"]
[24,"TCGA-A8-A099",5,null,70,"TCGA-C8-A8HP",4,"Eosin too heavy"]
[25,"TCGA-A8-A09E",5,null,71,"TCGA-D8-A1JA",4,"Pale/faded"]
[26,"TCGA-A8-A09I",5,null,72,"TCGA-D8-A1XJ",4,"Eosin too heavy"]
[27,"TCGA-A8-A09N",4,"Eosin weak",73,"TCGA-D8-A1XT",4,"Central tumour underfixed/autolysis"]
[28,"TCGA-A8-A0AB",4,"Eosin heavy",74,"TCGA-E2-A14P",5]
[29,"TCGA-AC-A23G",3,"Patchy degeneration of tumour and overstained",75,"TCGA-E2-A152",5]
[30,"TCGA-AC-A3QQ",4,"Weak haematoxylin",76,"TCGA-E2-A1B0",5]
[31,"TCGA-AC-A3YI",4,"Eosin too heavy, heamatoxylin weak",77,"TCGA-E2-A1LE",5]
[32,"TCGA-AC-A8OS",4,"Eosin weak",78,"TCGA-E9-A22D",5]
[33,"TCGA-AN-A0AK",4,"Haematoxylin heavy",79,"TCGA-E9-A22E",3,"Poor fixation/autolysis"]
[34,"TCGA-AN-A0FD",4,"Eosin weak",80,"TCGA-E9-A22G",5]
[35,"TCGA-AN-A0FJ",4,"Overstained (haematoxylin and eosin)",81,"TCGA-E9-A295",4,"Some autolysis"]
[36,"TCGA-AN-A0FK",5,null,82,"TCGA-EW-A1J3",3,"Very overstained"]
[37,"TCGA-AN-A0FL",4,"Overstained (haematoxylin and eosin)",83,"TCGA-EW-A424",4,"Overstained"]
[38,"TCGA-AN-A0FN",4,"Haematoxylin heavy",84,"TCGA-EW-A6S9",5]
[39,"TCGA-AN-A0FS",4,"Haematoxylin heavy",85,"TCGA-JL-A3YX",1,"Autolysed and overstained"]
[40,"TCGA-AN-A0FV",5,null,86,"TCGA-LD-A9QF",5]
[41,"TCGA-AN-A0FX",5,null,87,"TCGA-LL-A9Q3",4,"Haematoxylin too heavy"]
[42,"TCGA-AN-A0FZ",5,null,88,"TCGA-PE-A5DC",2,"Autolysed and overstained"]
[43,"TCGA-AN-A0XP",4,"Eosin too heavy",89,"TCGA-PE-A5DD",3,"Very overstained"]
[44,"TCGA-AN-A0XW",5,null,90,"TCGA-S3-AA14",4,"Bit overstained"]
[45,"TCGA-AO-A03L",3,"Eosin very heavy",91,"TCGA-UL-AAZ6",4,"Bit overstained"]
[46,"TCGA-AO-A0JE",4,"Overstained (haematoxylin and eosin)",92,"TCGA-UU-A93S",3,"Chatter artefact and overstained"]

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["Supplementary Table 2: pval of differential spatial gene expression test between selected 2,177 CNA genes and 280 genes NN correlation"]
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{"sheet":"Supplementary Table3","index":2,"n_rows":2179,"n_cols":281,"rows_kept":281,"cut":true,"merged":[[0,0,0,9]],"bounds":{"rows_first":125,"rows_last":31,"rows_between":125,"halvings":4}}
["Supplementary Table 3: fold change of NN correlation between gain and loss of 2,177 CNA genes"]
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{"sheet":"Supplementary Table 4","index":3,"n_rows":28,"n_cols":2,"rows_kept":28,"merged":[[1,1,1,2],[2,0,2,2],[3,1,3,2],[4,0,4,2],[5,1,5,2],[6,1,6,2],[7,0,7,2],[8,1,8,2],[9,1,9,2],[10,1,10,2],[11,0,11,2],[12,1,12,2],[13,1,13,2],[14,1,14,2],[15,0,15,2],[16,1,16,2],[17,1,17,2],[18,1,18,2],[19,0,19,2],[20,1,20,2],[21,1,21,2],[22,0,22,2],[23,1,23,2],[24,0,24,2],[25,1,25,2],[26,1,26,2],[27,1,27,2]]}
["Supplementary Table 4: Breast cancer tissue cohort summary"]
[null,"Mixed DCIS (n=44)"]
["Age (years)"]
["Mean (min-max)","51 (29-79)"]
["Grade"]
["Non-high grade","17 (39%)"]
["High grade","27 (62%)"]
["ER status"]
["Positive","35 (80%)"]
["Negative","9 (20%)"]
["Unknown","0 (0%)"]
["PR status"]
["Positive","32 (73%)"]
["Negative","10 (23%)"]
["Unknown","2 (5%)"]
["HER2 status"]
["Positive","12 (27%)"]
["Negative","31 (71%)"]
["Unknown","1 (2%)"]
["Follow-up data"]
["Data available","36 (82%)"]
["Lost to follow-up","8 (18%)"]
["Follow-up interval (months)"]
["Mean (min-max)","67 (17-146)"]
["Events"]
["Recurrences","9 (20%)"]
["Breast cancer specific deaths","6 (14%)"]
["No events","29 (66%)"]

{"sheet":"Supplementary Table 5","index":4,"n_rows":11,"n_cols":4,"rows_kept":11}
["Supplementary Table 5: Description and information on each feature type generated on the TCGA selected patients."]
[]
["Type of features","Brief description","Number of features","Example of names of specific features"]
["Proportion_raw","Cell type proportion for a given samples",9,"“Epithelial”, “Stromal”"]
["Proportion_ratio","Ratio of pairwise cell type proportion",36,"\"Malignant-vs-T\", \"Malignant-vs-Macrophage\""]
["Gene_mean_celltype","Average gene expression values within each cell type (280 genes x 9 cell types)",1620,"\"Malignant--SERHL2\" \"Malignant--TACSTD2\""]
["Gene_cor-celltype","Correlation of pairwise gene expression within each cell type",3248,"\"Malignant--SERHL2-with-TACSTD2\", \"Malignant--SERHL2-with-SERPINA3\""]
["L_stats","Describes whether two cell types are mixed or dispersed, a lower value indicates dispersed pattern, a higher value indicates a mixing pattern",81,"\"Malignant_T\", \"Malignant_Macrophage\""]
["Celltype_interaction","Cell type composition of neighbouring environment",43,"\"Malignant_T\", \"Malignant_Macrophage\""]
["Morans_I","A measure of spatial autocorrelation of gene expression, a lower value indicates random patterning of gene expression, a higher value indicates a clustering pattern.",280,"\"ABCC11\" \"ACTA2\""]
["NN_correlation","Stands for nearest neighbour correlation: Pearson correlation of gene expression with neighbouring cells.",280,"\"ABCC11\" \"ACTA2\""]