supplemental_material

Attachment 'Edge_Disease.txt'

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   1 ####################################################
   2 #This is the Cancer-frequency.NA file.
   3 #Commented lines (#) must be deleted before use.
   4 #You must change the extension from .txt to .NA before importing with Cytoscape.
   5 #This file attributes Cancers (nodes) with their frequency. 
   6 ####################Save this part in file and convert 54,4% to 0.54##############################
   7 
   8 Cancer	Altered of cases
   9 Serous Ovarian Cancer (TCGA) 	54,40%
  10 Bladder Urothelial Carcinoma (TCGA, Provisional) 	44,70%
  11 Lung Squamous Cell Carcinoma (TCGA, Provisional) 	41,60%
  12 Cervical Squamous Cell Carcinoma (TCGA, Provisional) 	36,10%
  13 Colon and Rectum Adenocarcinoma (TCGA, Provisional 	35,80%
  14 Breast Invasive Carcinoma (TCGA, Provisional) 	31,90%
  15 Lung Adenocarcinoma (TCGA, Provisional) 	29,00%
  16 Head and Neck Squamous Cell Carcinoma (TCGA, Provisional) 	26,70%
  17 Stomach Adenocarcinoma (TCGA, Provisional) 	26,50%
  18 Sarcoma (MSKCC/Broad) 	24,80%
  19 Liver Hepatocellular Carcinoma (TCGA, Provisional) 	20,80%
  20 Brain Lower Grade Glioma (TCGA, Provisional) 	12,50%
  21 Prostate Adenocarcinoma (TCGA, Provisional) 	12,20%
  22 Uterine Corpus Endometrioid Carcinoma (TCGA, Provisional) 	10,80%
  23 Prostate Cancer (MSKCC) 	8,20%
  24 Glioblastoma (TCGA) 	7,40%
  25 Kidney Renal Clear Cell Carcinoma (TCGA, Provisional) 	7,30%
  26 Pancreatic Adenocarcinoma (TCGA, Provisional) 	7,10%
  27 Kidney Renal Papillary Cell Carcinoma (TCGA, Provisional)	7,00%
  28 Thyroid Carcinoma (TCGA, Provisional) . 	2,40%
  29 
  30 ###########The following part exist yet in correlation+Cancer.txt file###########################
  31 ###########Save this part in an other file and convert comma to point############################
  32 
  33 #This is the second part of the correlation+Cancer.txt file .
  34 #Commented lines (#) must be deleted before use.
  35 #You must change the extension from .txt to .EA before importing with Cytoscape.
  36 #This file attributes values to interactions (Edges). Thers is two types of interactions: gene-#gene and gene-cancer.
  37 #This part existe in the correlation+Cancer.txt file
  38 #####################################
  39 Serous Ovarian Cancer (TCGA)/All Complete Tumors: (316)				PERCENT_CASES_ALTERED
  40 Ovarian_C (class=java.lang.Double)				
  41 TF	+%28pp%29+	Ovarian_C	=	0,92
  42 PPBP	+%28pp%29+	Ovarian_C	=	0,91
  43 CFHR2	+%28pp%29+	Ovarian_C	=	0,896
  44 CRP	+%28pp%29+	Ovarian_C	=	0,886
  45 CFHR1	+%28pp%29+	Ovarian_C	=	0,883
  46 RBP4	+%28pp%29+	Ovarian_C	=	0,877
  47 PRAP1	+%28pp%29+	Ovarian_C	=	0,858
  48 ADH4	+%28pp%29+	Ovarian_C	=	0,832
  49 LGALS3BP	+%28pp%29+	Ovarian_C	=	0,829
  50 COMP	+%28pp%29+	Ovarian_C	=	0,797
  51 YWHAZ	+%28pp%29+	Ovarian_C	=	0,491
  52 TFRC	+%28pp%29+	Ovarian_C	=	0,326
  53 TPM4	+%28pp%29+	Ovarian_C	=	0,253
  54 VCP	+%28pp%29+	Ovarian_C	=	0,168
  55 S100A8	+%28pp%29+	Ovarian_C	=	0,161
  56 HSPG2	+%28pp%29+	Ovarian_C	=	0,155
  57 PZP	+%28pp%29+	Ovarian_C	=	0,149
  58 ACTB	+%28pp%29+	Ovarian_C	=	0,142
  59 RAP1A	+%28pp%29+	Ovarian_C	=	0,142
  60 BPIFB1	+%28pp%29+	Ovarian_C	=	0,092
  61 ACTN1	+%28pp%29+	Ovarian_C	=	0,085
  62 GC	+%28pp%29+	Ovarian_C	=	0,063
  63 ORM2	+%28pp%29+	Ovarian_C	=	0,063
  64 KLKB1	+%28pp%29+	Ovarian_C	=	0,057
  65 ITIH3	+%28pp%29+	Ovarian_C	=	0,051
  66 HBA1	+%28pp%29+	Ovarian_C	=	0
  67 IGHD	+%28pp%29+	Ovarian_C	=	0
  68 				
  69 GENE_SYMBOL	NUM_CASES_ALTERED	PERCENT_CASES_ALTERED		178 samples
  70 Lunch.Sq_C (class=java.lang.Double)				
  71 ADH4	+%28pp%29+	Lunch.Sq_C	=	0,989
  72 CFHR2	+%28pp%29+	Lunch.Sq_C	=	0,983
  73 PPBP	+%28pp%29+	Lunch.Sq_C	=	0,983
  74 PRAP1	+%28pp%29+	Lunch.Sq_C	=	0,983
  75 CRP	+%28pp%29+	Lunch.Sq_C	=	0,966
  76 HBA1	+%28pp%29+	Lunch.Sq_C	=	0,961
  77 TF	+%28pp%29+	Lunch.Sq_C	=	0,938
  78 COMP	+%28pp%29+	Lunch.Sq_C	=	0,921
  79 RBP4	+%28pp%29+	Lunch.Sq_C	=	0,921
  80 CFHR1	+%28pp%29+	Lunch.Sq_C	=	0,854
  81 LGALS3BP	+%28pp%29+	Lunch.Sq_C	=	0,803
  82 TFRC	+%28pp%29+	Lunch.Sq_C	=	0,612
  83 ACTB	+%28pp%29+	Lunch.Sq_C	=	0,264
  84 YWHAZ	+%28pp%29+	Lunch.Sq_C	=	0,242
  85 VCP	+%28pp%29+	Lunch.Sq_C	=	0,23
  86 TPM4	+%28pp%29+	Lunch.Sq_C	=	0,146
  87 ACTN1	+%28pp%29+	Lunch.Sq_C	=	0,135
  88 RAP1A	+%28pp%29+	Lunch.Sq_C	=	0,129
  89 ORM2	+%28pp%29+	Lunch.Sq_C	=	0,101
  90 PZP	+%28pp%29+	Lunch.Sq_C	=	0,101
  91 KLKB1	+%28pp%29+	Lunch.Sq_C	=	0,096
  92 HSPG2	+%28pp%29+	Lunch.Sq_C	=	0,09
  93 ITIH3	+%28pp%29+	Lunch.Sq_C	=	0,084
  94 S100A8	+%28pp%29+	Lunch.Sq_C	=	0,073
  95 BPIFB1	+%28pp%29+	Lunch.Sq_C	=	0,056
  96 GC	+%28pp%29+	Lunch.Sq_C	=	0,034
  97 IGHD	+%28pp%29+	Lunch.Sq_C	=	0
  98 				
  99 				
 100 GENE_SYMBOL	NUM_CASES_ALTERED	PERCENT_CASES_ALTERED		193 samples
 101 Colon_C  (class=java.lang.Double)				
 102 CRP	+%28pp%29+	Colon_C	=	0,995
 103 PPBP	+%28pp%29+	Colon_C	=	0,984
 104 TF	+%28pp%29+	Colon_C	=	0,948
 105 CFHR1	+%28pp%29+	Colon_C	=	0,933
 106 COMP	+%28pp%29+	Colon_C	=	0,933
 107 ADH4	+%28pp%29+	Colon_C	=	0,912
 108 HBA1	+%28pp%29+	Colon_C	=	0,896
 109 RBP4	+%28pp%29+	Colon_C	=	0,886
 110 PRAP1	+%28pp%29+	Colon_C	=	0,881
 111 LGALS3BP	+%28pp%29+	Colon_C	=	0,86
 112 YWHAZ	+%28pp%29+	Colon_C	=	0,326
 113 TFRC	+%28pp%29+	Colon_C	=	0,192
 114 VCP	+%28pp%29+	Colon_C	=	0,187
 115 TPM4	+%28pp%29+	Colon_C	=	0,166
 116 RAP1A	+%28pp%29+	Colon_C	=	0,145
 117 HSPG2	+%28pp%29+	Colon_C	=	0,119
 118 ACTN1	+%28pp%29+	Colon_C	=	0,109
 119 ACTB	+%28pp%29+	Colon_C	=	0,088
 120 KLKB1	+%28pp%29+	Colon_C	=	0,083
 121 PZP	+%28pp%29+	Colon_C	=	0,078
 122 ITIH3	+%28pp%29+	Colon_C	=	0,067
 123 ORM2	+%28pp%29+	Colon_C	=	0,052
 124 S100A8	+%28pp%29+	Colon_C	=	0,052
 125 BPIFB1	+%28pp%29+	Colon_C	=	0,031
 126 GC	+%28pp%29+	Colon_C	=	0,031
 127 CFHR2	+%28pp%29+	Colon_C	=	0
 128 IGHD	+%28pp%29+	Colon_C	=	0
 129 				
 130 				
 131 GENE_SYMBOL	NUM_CASES_ALTERED	PERCENT_CASES_ALTERED		320 samples
 132 Breast_C	(class=java.lang.Double)			
 133 CFHR2	+%28pp%29+	Breast_C	=	0,991
 134 PPBP	+%28pp%29+	Breast_C	=	0,978
 135 TF	+%28pp%29+	Breast_C	=	0,969
 136 ADH4	+%28pp%29+	Breast_C	=	0,962
 137 PRAP1	+%28pp%29+	Breast_C	=	0,941
 138 HBA1	+%28pp%29+	Breast_C	=	0,925
 139 CRP	+%28pp%29+	Breast_C	=	0,919
 140 RBP4	+%28pp%29+	Breast_C	=	0,919
 141 COMP	+%28pp%29+	Breast_C	=	0,903
 142 CFHR1	+%28pp%29+	Breast_C	=	0,862
 143 LGALS3BP	+%28pp%29+	Breast_C	=	0,781
 144 YWHAZ	+%28pp%29+	Breast_C	=	0,441
 145 ACTB	+%28pp%29+	Breast_C	=	0,194
 146 TFRC	+%28pp%29+	Breast_C	=	0,194
 147 TPM4	+%28pp%29+	Breast_C	=	0,159
 148 VCP	+%28pp%29+	Breast_C	=	0,159
 149 ACTN1	+%28pp%29+	Breast_C	=	0,141
 150 HSPG2	+%28pp%29+	Breast_C	=	0,131
 151 RAP1A	+%28pp%29+	Breast_C	=	0,122
 152 KLKB1	+%28pp%29+	Breast_C	=	0,094
 153 PZP	+%28pp%29+	Breast_C	=	0,084
 154 S100A8	+%28pp%29+	Breast_C	=	0,072
 155 ITIH3	+%28pp%29+	Breast_C	=	0,056
 156 BPIFB1	+%28pp%29+	Breast_C	=	0,053
 157 ORM2	+%28pp%29+	Breast_C	=	0,022
 158 GC	+%28pp%29+	Breast_C	=	0
 159 IGHD	+%28pp%29+	Breast_C	=	0
 160 				
 161             				
 162 GENE_SYMBOL	NUM_CASES_ALTERED	PERCENT_CASES_ALTERED		85 samples
 163 Prostate_C	(class=java.lang.Double)			
 164 LGALS3BP	+%28pp%29+	Prostate_C	=	0,953
 165 RBP4	+%28pp%29+	Prostate_C	=	0,929
 166 TF	+%28pp%29+	Prostate_C	=	0,929
 167 COMP	+%28pp%29+	Prostate_C	=	0,882
 168 CFHR1	+%28pp%29+	Prostate_C	=	0,871
 169 ADH4	+%28pp%29+	Prostate_C	=	0,859
 170 CRP	+%28pp%29+	Prostate_C	=	0,776
 171 HBA1	+%28pp%29+	Prostate_C	=	0,776
 172 PRAP1	+%28pp%29+	Prostate_C	=	0,776
 173 PPBP	+%28pp%29+	Prostate_C	=	0,765
 174 CFHR2	+%28pp%29+	Prostate_C	=	0,624
 175 S100A8	+%28pp%29+	Prostate_C	=	0,271
 176 TFRC	+%28pp%29+	Prostate_C	=	0,271
 177 GC	+%28pp%29+	Prostate_C	=	0,259
 178 BPIFB1	+%28pp%29+	Prostate_C	=	0,247
 179 ITIH3	+%28pp%29+	Prostate_C	=	0,235
 180 YWHAZ	+%28pp%29+	Prostate_C	=	0,188
 181 KLKB1	+%28pp%29+	Prostate_C	=	0,153
 182 PZP	+%28pp%29+	Prostate_C	=	0,141
 183 VCP	+%28pp%29+	Prostate_C	=	0,141
 184 ORM2	+%28pp%29+	Prostate_C	=	0,106
 185 RAP1A	+%28pp%29+	Prostate_C	=	0,071
 186 TPM4	+%28pp%29+	Prostate_C	=	0,071
 187 ACTB	+%28pp%29+	Prostate_C	=	0,035
 188 ACTN1	+%28pp%29+	Prostate_C	=	0
 189 HSPG2	+%28pp%29+	Prostate_C	=	0
 190 IGHD	+%28pp%29+	Prostate_C	=	0
 191 				
 192             				
 193 				
 194 GENE_SYMBOL	NUM_CASES_ALTERED	PERCENT_CASES_ALTERED		122 samples
 195 Glioblastoma_C	(class=java.lang.Double)			
 196 CFHR2	+%28pp%29+	Glioblastoma_C	=	0,934
 197 ADH4	+%28pp%29+	Glioblastoma_C	=	0,877
 198 CFHR1	+%28pp%29+	Glioblastoma_C	=	0,861
 199 RBP4	+%28pp%29+	Glioblastoma_C	=	0,861
 200 CRP	+%28pp%29+	Glioblastoma_C	=	0,852
 201 PPBP	+%28pp%29+	Glioblastoma_C	=	0,836
 202 TF	+%28pp%29+	Glioblastoma_C	=	0,82
 203 COMP	+%28pp%29+	Glioblastoma_C	=	0,795
 204 PRAP1	+%28pp%29+	Glioblastoma_C	=	0,787
 205 LGALS3BP	+%28pp%29+	Glioblastoma_C	=	0,738
 206 TPM4	+%28pp%29+	Glioblastoma_C	=	0,361
 207 HSPG2	+%28pp%29+	Glioblastoma_C	=	0,18
 208 ITIH3	+%28pp%29+	Glioblastoma_C	=	0,164
 209 S100A8	+%28pp%29+	Glioblastoma_C	=	0,164
 210 VCP	+%28pp%29+	Glioblastoma_C	=	0,164
 211 KLKB1	+%28pp%29+	Glioblastoma_C	=	0,156
 212 ACTN1	+%28pp%29+	Glioblastoma_C	=	0,148
 213 PZP	+%28pp%29+	Glioblastoma_C	=	0,139
 214 BPIFB1	+%28pp%29+	Glioblastoma_C	=	0,131
 215 ACTB	+%28pp%29+	Glioblastoma_C	=	0,082
 216 TFRC	+%28pp%29+	Glioblastoma_C	=	0,066
 217 YWHAZ	+%28pp%29+	Glioblastoma_C	=	0,066
 218 ORM2	+%28pp%29+	Glioblastoma_C	=	0,057
 219 RAP1A	+%28pp%29+	Glioblastoma_C	=	0,041
 220 GC	+%28pp%29+	Glioblastoma_C	=	0,025
 221 HBA1	+%28pp%29+	Glioblastoma_C	=	0
 222 IGHD	+%28pp%29+	Glioblastoma_C	=	0
 223 				
 224 				
 225 Kidney Renal Clear Cell Carcinoma (TCGA, Provisional)				
 226 				
 227 				
 228 GENE_SYMBOL	NUM_CASES_ALTERED	PERCENT_CASES_ALTERED		368 samples
 229 Kidney_C	(class=java.lang.Double)			
 230 ADH4	+%28pp%29+	Kidney_C	=	0,997
 231 CFHR2	+%28pp%29+	Kidney_C	=	0,984
 232 CRP	+%28pp%29+	Kidney_C	=	0,978
 233 TF	+%28pp%29+	Kidney_C	=	0,973
 234 PPBP	+%28pp%29+	Kidney_C	=	0,962
 235 COMP	+%28pp%29+	Kidney_C	=	0,94
 236 HBA1	+%28pp%29+	Kidney_C	=	0,938
 237 RBP4	+%28pp%29+	Kidney_C	=	0,921
 238 PRAP1	+%28pp%29+	Kidney_C	=	0,908
 239 CFHR1	+%28pp%29+	Kidney_C	=	0,87
 240 LGALS3BP	+%28pp%29+	Kidney_C	=	0,818
 241 ACTB	+%28pp%29+	Kidney_C	=	0,16
 242 TFRC	+%28pp%29+	Kidney_C	=	0,158
 243 TPM4	+%28pp%29+	Kidney_C	=	0,152
 244 ACTN1	+%28pp%29+	Kidney_C	=	0,147
 245 YWHAZ	+%28pp%29+	Kidney_C	=	0,147
 246 VCP	+%28pp%29+	Kidney_C	=	0,13
 247 ITIH3	+%28pp%29+	Kidney_C	=	0,12
 248 BPIFB1	+%28pp%29+	Kidney_C	=	0,114
 249 HSPG2	+%28pp%29+	Kidney_C	=	0,109
 250 KLKB1	+%28pp%29+	Kidney_C	=	0,101
 251 PZP	+%28pp%29+	Kidney_C	=	0,084
 252 RAP1A	+%28pp%29+	Kidney_C	=	0,082
 253 S100A8	+%28pp%29+	Kidney_C	=	0,049
 254 GC	+%28pp%29+	Kidney_C	=	0,041
 255 ORM2	+%28pp%29+	Kidney_C	=	0,014
 256 IGHD	+%28pp%29+	Kidney_C	=	0

Attached Files

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  • [get | view] (2012-12-22 11:05:34, 1.7 KB) [[attachment:Cancer_Network.txt]]
  • [get | view] (2012-12-22 11:08:11, 0.7 KB) [[attachment:Cancer_frequency.txt]]
  • [get | view] (2012-12-22 11:01:12, 24.4 KB) [[attachment:Correlation+Cancers.txt]]
  • [get | view] (2012-12-22 10:55:11, 8.4 KB) [[attachment:Correlation_Network.txt]]
  • [get | view] (2012-12-22 11:22:48, 9.2 KB) [[attachment:Edge_Disease.txt]]
  • [get | view] (2012-12-22 10:58:31, 3.7 KB) [[attachment:FDR.txt]]
  • [get | view] (2012-12-24 11:47:48, 351.0 KB) [[attachment:Figure 1.eps]]
  • [get | view] (2012-12-24 11:51:49, 3087.6 KB) [[attachment:Figure 2.eps]]
  • [get | view] (2012-12-24 11:55:50, 314.0 KB) [[attachment:Figure 3.eps]]
  • [get | view] (2012-12-22 10:56:27, 3.4 KB) [[attachment:Fold_Change.txt]]
  • [get | view] (2013-04-03 19:57:12, 57.0 KB) [[attachment:Patient-profile.png]]
  • [get | view] (2012-12-24 10:52:22, 71.2 KB) [[attachment:Supplemental_Table 2.pdf]]
  • [get | view] (2013-04-03 22:21:23, 98.3 KB) [[attachment:Supplemental_Table1.pdf]]
  • [get | view] (2013-04-03 20:56:13, 4067.5 KB) [[attachment:Supplemental_Tutorial.pdf]]
  • [get | view] (2012-12-22 11:24:10, 217.2 KB) [[attachment:network.cys]]
  • [get | view] (2012-12-22 11:32:20, 0.7 KB) [[attachment:only_modulatedEXP.txt]]
  • [get | view] (2012-12-24 19:11:00, 0.3 KB) [[attachment:only_modulated_symbol.txt]]
  • [get | view] (2012-12-22 11:30:53, 11.0 KB) [[attachment:proteinEXP.txt]]
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