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    v0.1 cell line networks
    v0.2 aggregate tissue networks
    v0.3 TF enrichement tool
    v0.4 single-sample tissue networks
    v0.5 CLUEreg tool
    v0.6 colon cancer networks
    v0.7 drug networks
    v0.7.1 API v1
    v0.8 liver, cervix, and breast cancer networks
    v0.9 miRNA tissue networks
    v0.9.1 bootstrap 5
    v1.0 glioblastoma networks

    Tool description

    PANDA reconstructs a gene regulatory network using TF PPI, TF DNA binding motif as regulation prior, and gene expression samples. PUMA reconstructs a gene regulatory network with miRNA as regulators using gene expression samples and miRNA predicted targets by miRanda or TargetScan as regulation priors. The Regulator-regulator interaction matrix is set to the identity matrix in the algorithm. LIONESS reconstructs patient-specific PANDA networks for each gene expression sample. To download sample-specific networks, you can check the phenotypic information and select the networks by clinical variables or download all the samples in a single file.

    Publication
    Please check the reference Sonawane et al. (2017) at the following link.
    Publication
    Please check the reference Lopes-Ramos et al. (2020) at the following link.
    Publication
    Please check the reference Kuijjer et al. (2020) at the following link.
    Publication
    Please check the reference Kuijjer et al. (2020) at the following link.
    # Tissue Tool netZoo release Network
    		PPI
    		 Reg. prior Expr.
    		 Reg.
    		 nReg
    		 Genes Samples Precision
    		 Reference
    1 Intestine terminal ileum PANDA netZooM 0.1
    coR
    		 Motif TF 644 30243 104 D
    2 Intestine terminal ileum PANDA-LIONESS netZooM 0.1
    coR
    		 Motif TF 644 30243 104 D
    3 Intestine terminal ileum PUMA netZooM 0.3
    coR
    		 - miRanda miRNA 643 16161 267 D
    4 Intestine terminal ileum PUMA netZooM 0.3
    coR
    		 - TargetScan miRNA 643 16161 267 D

    Variable description

    You can either download all the networks to get a matrix of size the number of samples by the number of edges. The number of edges is 644 * 30243 (number of TFs * number of genes) (~ 106). Otherwise, you can specify the sample network to download and you will get a TF-by-gene matrix named after the GTEx sample reference.

    Sample Subject Gender
    		Age DTH-HRDY
    		 SMAT-SSCR
    		 SMRIN
    		 SMTS
    		 SMTSD
    		 SMUBRID
    		 SMTSISCH
    		 Network
    All All - - - - - - - - - po
    34 GB
    GTEX-111CU-1326-SM-5NQ8L GTEX-111CU 1 50-59 0 0 7.5 Small Intestine Small Intestine - Terminal Ileum 1211 94 co
    369 MB
    GTEX-111YS-1426-SM-5GID8 GTEX-111YS 1 60-69 0 0 7 Small Intestine Small Intestine - Terminal Ileum 1211 158 co
    369 MB
    GTEX-1122O-1326-SM-5H11F GTEX-1122O 2 60-69 0 0 7.3 Small Intestine Small Intestine - Terminal Ileum 1211 103 co
    369 MB
    GTEX-117YX-0326-SM-5GICL GTEX-117YX 1 50-59 0 1 8 Small Intestine Small Intestine - Terminal Ileum 1211 84 co
    369 MB
    GTEX-1192X-2526-SM-59868 GTEX-1192X 1 50-59 4 3 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 952 co
    369 MB
    GTEX-11DXX-1626-SM-5H11H GTEX-11DXX 2 60-69 0 1 7.3 Small Intestine Small Intestine - Terminal Ileum 1211 124 co
    369 MB
    GTEX-11DXZ-1326-SM-5H11X GTEX-11DXZ 1 50-59 0 1 6.7 Small Intestine Small Intestine - Terminal Ileum 1211 302 co
    369 MB
    GTEX-11EQ9-1326-SM-5985X GTEX-11EQ9 1 30-39 2 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 113 co
    369 MB
    GTEX-11I78-1126-SM-5A5K5 GTEX-11I78 2 50-59 0 1 6.6 Small Intestine Small Intestine - Terminal Ileum 1211 109 co
    369 MB
    GTEX-11LCK-1926-SM-5A5KE GTEX-11LCK 1 30-39 0 2 7.1 Small Intestine Small Intestine - Terminal Ileum 1211 349 co
    369 MB
    GTEX-11NSD-1726-SM-5N9C3 GTEX-11NSD 1 20-29 0 1 7.9 Small Intestine Small Intestine - Terminal Ileum 1211 136 co
    369 MB
    GTEX-11P7K-1626-SM-5GU63 GTEX-11P7K 1 30-39 0 1 8.5 Small Intestine Small Intestine - Terminal Ileum 1211 158 co
    369 MB
    GTEX-11P82-0826-SM-5P9GU GTEX-11P82 1 20-29 1 1 8.4 Small Intestine Small Intestine - Terminal Ileum 1211 165 co
    369 MB
    GTEX-11TUW-1926-SM-5BC58 GTEX-11TUW 1 60-69 2 3 6 Small Intestine Small Intestine - Terminal Ileum 1211 770 co
    369 MB
    GTEX-11VI4-1626-SM-5EQKO GTEX-11VI4 2 40-49 0 1 8.2 Small Intestine Small Intestine - Terminal Ileum 1211 177 co
    369 MB
    GTEX-11WQK-2326-SM-5GU4Z GTEX-11WQK 1 50-59 2 3 6.3 Small Intestine Small Intestine - Terminal Ileum 1211 806 co
    369 MB
    GTEX-11XUK-1426-SM-5EQMG GTEX-11XUK 2 40-49 0 1 7.7 Small Intestine Small Intestine - Terminal Ileum 1211 164 co
    369 MB
    GTEX-12BJ1-1926-SM-5HL9Z GTEX-12BJ1 1 60-69 0 1 7.1 Small Intestine Small Intestine - Terminal Ileum 1211 162 co
    369 MB
    GTEX-12WSK-1526-SM-5CVNO GTEX-12WSK 2 40-49 0 2 6 Small Intestine Small Intestine - Terminal Ileum 1211 182 co
    369 MB
    GTEX-13111-1426-SM-5DUW3 GTEX-13111 1 50-59 0 1 6.4 Small Intestine Small Intestine - Terminal Ileum 1211 308 co
    369 MB
    GTEX-13113-1226-SM-5EGHT GTEX-13113 2 60-69 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 249 co
    369 MB
    GTEX-131XE-0926-SM-5HL7J GTEX-131XE 1 50-59 0 1 6.8 Small Intestine Small Intestine - Terminal Ileum 1211 197 co
    369 MB
    GTEX-131XF-1326-SM-5GCMQ GTEX-131XF 1 60-69 0 1 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 253 co
    369 MB
    GTEX-131XG-1726-SM-5LZUR GTEX-131XG 2 50-59 0 2 7.5 Small Intestine Small Intestine - Terminal Ileum 1211 142 co
    369 MB
    GTEX-133LE-1426-SM-5IFH1 GTEX-133LE 2 20-29 0 1 6.6 Small Intestine Small Intestine - Terminal Ileum 1211 178 co
    369 MB
    GTEX-1399R-2026-SM-5K7WN GTEX-1399R 1 30-39 0 1 5.8 Small Intestine Small Intestine - Terminal Ileum 1211 155 co
    369 MB
    GTEX-1399S-2026-SM-5KM4B GTEX-1399S 2 30-39 0 1 8 Small Intestine Small Intestine - Terminal Ileum 1211 141 co
    369 MB
    GTEX-1399U-2126-SM-5IFEZ GTEX-1399U 2 50-59 0 2 7.1 Small Intestine Small Intestine - Terminal Ileum 1211 227 co
    369 MB
    GTEX-139T6-1026-SM-5IJGC GTEX-139T6 1 50-59 0 1 7.1 Small Intestine Small Intestine - Terminal Ileum 1211 171 co
    369 MB
    GTEX-139YR-2226-SM-5IFFW GTEX-139YR 1 50-59 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 232 co
    369 MB
    GTEX-13CF3-1226-SM-5LZXN GTEX-13CF3 2 60-69 0 1 6.6 Small Intestine Small Intestine - Terminal Ileum 1211 166 co
    369 MB
    GTEX-13D11-0726-SM-5LZZB GTEX-13D11 2 50-59 0 1 7.7 Small Intestine Small Intestine - Terminal Ileum 1211 102 co
    369 MB
    GTEX-13FH7-1226-SM-5IJFK GTEX-13FH7 2 50-59 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 138 co
    369 MB
    GTEX-13FTW-2026-SM-5IJE2 GTEX-13FTW 1 40-49 0 1 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 220 co
    369 MB
    GTEX-13NYB-1826-SM-5J1N3 GTEX-13NYB 1 40-49 2 3 5.8 Small Intestine Small Intestine - Terminal Ileum 1211 1063 co
    369 MB
    GTEX-13O21-1026-SM-5IJDU GTEX-13O21 1 50-59 0 1 6.4 Small Intestine Small Intestine - Terminal Ileum 1211 177 co
    369 MB
    GTEX-13O61-1326-SM-5KM31 GTEX-13O61 1 60-69 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 172 co
    369 MB
    GTEX-13OVI-1926-SM-5IJCG GTEX-13OVI 2 60-69 0 1 6.6 Small Intestine Small Intestine - Terminal Ileum 1211 224 co
    369 MB
    GTEX-13PL7-2626-SM-5IFH4 GTEX-13PL7 2 60-69 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 185 co
    369 MB
    GTEX-13QBU-1926-SM-5IJEW GTEX-13QBU 2 40-49 0 1 6.9 Small Intestine Small Intestine - Terminal Ileum 1211 236 co
    369 MB
    GTEX-13RTK-0826-SM-5Q5C6 GTEX-13RTK 1 20-29 0 2 7.8 Small Intestine Small Intestine - Terminal Ileum 1211 1682 co
    369 MB
    GTEX-13W3W-2026-SM-5K7UL GTEX-13W3W 2 60-69 0 1 7.5 Small Intestine Small Intestine - Terminal Ileum 1211 265 co
    369 MB
    GTEX-145LT-1026-SM-5LU9O GTEX-145LT 1 40-49 0 1 8.2 Small Intestine Small Intestine - Terminal Ileum 1211 186 co
    369 MB
    GTEX-145ME-0926-SM-5O9AR GTEX-145ME 2 40-49 0 1 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 281 co
    369 MB
    GTEX-148VJ-2226-SM-5NQ9M GTEX-148VJ 1 70-79 2 3 6.3 Small Intestine Small Intestine - Terminal Ileum 1211 1104 co
    369 MB
    GTEX-14DAR-1426-SM-5RQIR GTEX-14DAR 1 50-59 0 1 7.9 Small Intestine Small Intestine - Terminal Ileum 1211 145 co
    369 MB
    GTEX-14E6E-1626-SM-5RQI7 GTEX-14E6E 1 30-39 0 0 8 Small Intestine Small Intestine - Terminal Ileum 1211 164 co
    369 MB
    GTEX-UPK5-2026-SM-4JBIM GTEX-UPK5 1 40-49 0 1 7.1 Small Intestine Small Intestine - Terminal Ileum 1211 1015 co
    369 MB
    GTEX-VJYA-0926-SM-4KL1N GTEX-VJYA 1 60-69 0 1 7.6 Small Intestine Small Intestine - Terminal Ileum 1211 251 co
    369 MB
    GTEX-VUSG-1726-SM-4KKZL GTEX-VUSG 1 50-59 0 2 6.1 Small Intestine Small Intestine - Terminal Ileum 1211 223 co
    369 MB
    GTEX-WEY5-1526-SM-4LMJF GTEX-WEY5 2 40-49 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 271 co
    369 MB
    GTEX-WFG7-1726-SM-4LVME GTEX-WFG7 1 20-29 0 1 6.8 Small Intestine Small Intestine - Terminal Ileum 1211 192 co
    369 MB
    GTEX-WFG8-1626-SM-4LVMB GTEX-WFG8 1 20-29 0 1 8.6 Small Intestine Small Intestine - Terminal Ileum 1211 277 co
    369 MB
    GTEX-WFJO-0926-SM-4LVM2 GTEX-WFJO 1 30-39 0 1 7.9 Small Intestine Small Intestine - Terminal Ileum 1211 223 co
    369 MB
    GTEX-WFON-1526-SM-4LVMP GTEX-WFON 1 40-49 0 2 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 270 co
    369 MB
    GTEX-WH7G-1626-SM-4LVMY GTEX-WH7G 1 40-49 0 2 7.3 Small Intestine Small Intestine - Terminal Ileum 1211 318 co
    369 MB
    GTEX-WHSB-1026-SM-4M1XN GTEX-WHSB 1 50-59 0 1 7.8 Small Intestine Small Intestine - Terminal Ileum 1211 260 co
    369 MB
    GTEX-WQUQ-2426-SM-4MVNW GTEX-WQUQ 1 60-69 0 1 5.7 Small Intestine Small Intestine - Terminal Ileum 1211 507 co
    369 MB
    GTEX-WRHK-1026-SM-4MVOD GTEX-WRHK 2 20-29 0 1 7 Small Intestine Small Intestine - Terminal Ileum 1211 265 co
    369 MB
    GTEX-WY7C-1826-SM-4ONCE GTEX-WY7C 1 50-59 0 2 8.8 Small Intestine Small Intestine - Terminal Ileum 1211 210 co
    369 MB
    GTEX-WYJK-1526-SM-4ONCW GTEX-WYJK 1 50-59 0 1 7.9 Small Intestine Small Intestine - Terminal Ileum 1211 787 co
    369 MB
    GTEX-X15G-1426-SM-4PQZK GTEX-X15G 2 50-59 0 1 8.6 Small Intestine Small Intestine - Terminal Ileum 1211 271 co
    369 MB
    GTEX-X5EB-1626-SM-4E3IV GTEX-X5EB 1 40-49 0 1 7.8 Small Intestine Small Intestine - Terminal Ileum 1211 248 co
    369 MB
    GTEX-XAJ8-0526-SM-47JYK GTEX-XAJ8 1 40-49 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 138 co
    369 MB
    GTEX-XBED-1426-SM-4AT4G GTEX-XBED 1 60-69 0 1 8 Small Intestine Small Intestine - Terminal Ileum 1211 138 co
    369 MB
    GTEX-XGQ4-1326-SM-4GIDU GTEX-XGQ4 1 50-59 0 1 8.8 Small Intestine Small Intestine - Terminal Ileum 1211 173 co
    369 MB
    GTEX-XMK1-1826-SM-4B66F GTEX-XMK1 1 40-49 0 2 7.9 Small Intestine Small Intestine - Terminal Ileum 1211 228 co
    369 MB
    GTEX-XPVG-1726-SM-4B65W GTEX-XPVG 1 50-59 0 1 7.3 Small Intestine Small Intestine - Terminal Ileum 1211 156 co
    369 MB
    GTEX-XUZC-1426-SM-4BRV3 GTEX-XUZC 2 30-39 0 1 7.7 Small Intestine Small Intestine - Terminal Ileum 1211 136 co
    369 MB
    GTEX-XXEK-1026-SM-4BRUW GTEX-XXEK 1 50-59 0 1 6.6 Small Intestine Small Intestine - Terminal Ileum 1211 168 co
    369 MB
    GTEX-Y111-2226-SM-4SOJB GTEX-Y111 1 50-59 1 2 5.7 Small Intestine Small Intestine - Terminal Ileum 1211 1542 co
    369 MB
    GTEX-Y114-1426-SM-4TT6W GTEX-Y114 2 50-59 0 1 8.4 Small Intestine Small Intestine - Terminal Ileum 1211 154 co
    369 MB
    GTEX-Y3I4-1326-SM-4TT8Z GTEX-Y3I4 1 50-59 0 1 7.3 Small Intestine Small Intestine - Terminal Ileum 1211 149 co
    369 MB
    GTEX-Y3IK-1726-SM-4YCCR GTEX-Y3IK 2 50-59 0 2 6.4 Small Intestine Small Intestine - Terminal Ileum 1211 156 co
    369 MB
    GTEX-Y5LM-1626-SM-4VDTB GTEX-Y5LM 2 40-49 0 2 8.6 Small Intestine Small Intestine - Terminal Ileum 1211 154 co
    369 MB
    GTEX-Y5V5-1826-SM-4VDS5 GTEX-Y5V5 2 60-69 0 2 7.2 Small Intestine Small Intestine - Terminal Ileum 1211 228 co
    369 MB
    GTEX-Y9LG-1626-SM-5IFHM GTEX-Y9LG 1 30-39 0 1 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 129 co
    369 MB
    GTEX-YB5E-1526-SM-5IFIE GTEX-YB5E 1 40-49 0 1 8.6 Small Intestine Small Intestine - Terminal Ileum 1211 222 co
    369 MB
    GTEX-YEC4-1726-SM-4W21E GTEX-YEC4 1 40-49 0 1 7.6 Small Intestine Small Intestine - Terminal Ileum 1211 240 co
    369 MB
    GTEX-YF7O-1826-SM-5IFIU GTEX-YF7O 1 50-59 0 1 6.5 Small Intestine Small Intestine - Terminal Ileum 1211 178 co
    369 MB
    GTEX-Z9EW-0926-SM-5CVMM GTEX-Z9EW 1 40-49 0 1 6.7 Small Intestine Small Intestine - Terminal Ileum 1211 219 co
    369 MB
    GTEX-ZA64-1226-SM-5HL7B GTEX-ZA64 1 20-29 0 1 7.2 Small Intestine Small Intestine - Terminal Ileum 1211 141 co
    369 MB
    GTEX-ZAB5-1526-SM-5HL9P GTEX-ZAB5 1 50-59 0 0 8.2 Small Intestine Small Intestine - Terminal Ileum 1211 213 co
    369 MB
    GTEX-ZC5H-2326-SM-4WAYT GTEX-ZC5H 2 40-49 0 2 7.2 Small Intestine Small Intestine - Terminal Ileum 1211 323 co
    369 MB
    GTEX-ZEX8-1826-SM-57WBH GTEX-ZEX8 1 50-59 0 1 7.2 Small Intestine Small Intestine - Terminal Ileum 1211 151 co
    369 MB
    GTEX-ZF29-1626-SM-4WKFJ GTEX-ZF29 2 60-69 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 140 co
    369 MB
    GTEX-ZF2S-1726-SM-57WFT GTEX-ZF2S 2 50-59 0 1 8.3 Small Intestine Small Intestine - Terminal Ileum 1211 150 co
    369 MB
    GTEX-ZLFU-1526-SM-4WWBT GTEX-ZLFU 1 40-49 0 0 8 Small Intestine Small Intestine - Terminal Ileum 1211 154 co
    369 MB
    GTEX-ZLV1-1126-SM-4WWBW GTEX-ZLV1 2 60-69 0 1 7.1 Small Intestine Small Intestine - Terminal Ileum 1211 1574 co
    369 MB
    GTEX-ZP4G-1626-SM-57WGD GTEX-ZP4G 2 20-29 0 1 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 229 co
    369 MB
    GTEX-ZPCL-1726-SM-57WEO GTEX-ZPCL 2 60-69 0 1 8.4 Small Intestine Small Intestine - Terminal Ileum 1211 128 co
    369 MB
    GTEX-ZPIC-2326-SM-57WDW GTEX-ZPIC 2 40-49 0 2 7.5 Small Intestine Small Intestine - Terminal Ileum 1211 182 co
    369 MB
    GTEX-ZQG8-2526-SM-57WEQ GTEX-ZQG8 2 60-69 0 1 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 196 co
    369 MB
    GTEX-ZQUD-0926-SM-57WE3 GTEX-ZQUD 1 30-39 0 1 8.1 Small Intestine Small Intestine - Terminal Ileum 1211 205 co
    369 MB
    GTEX-ZTPG-2626-SM-57WFX GTEX-ZTPG 2 20-29 0 1 7 Small Intestine Small Intestine - Terminal Ileum 1211 293 co
    369 MB
    GTEX-ZTSS-0926-SM-59865 GTEX-ZTSS 1 40-49 0 1 7.2 Small Intestine Small Intestine - Terminal Ileum 1211 197 co
    369 MB
    GTEX-ZTX8-0526-SM-59HLD GTEX-ZTX8 1 20-29 0 1 8 Small Intestine Small Intestine - Terminal Ileum 1211 144 co
    369 MB
    GTEX-ZVP2-1726-SM-5GU5P GTEX-ZVP2 1 50-59 0 1 7.1 Small Intestine Small Intestine - Terminal Ileum 1211 157 co
    369 MB
    GTEX-ZVT2-2126-SM-5NQ93 GTEX-ZVT2 2 50-59 0 1 7.4 Small Intestine Small Intestine - Terminal Ileum 1211 127 co
    369 MB
    GTEX-ZVZP-1826-SM-5GZXB GTEX-ZVZP 1 50-59 0 1 6.5 Small Intestine Small Intestine - Terminal Ileum 1211 123 co
    369 MB
    GTEX-ZXES-1526-SM-5NQ95 GTEX-ZXES 2 30-39 0 1 8 Small Intestine Small Intestine - Terminal Ileum 1211 120 co
    369 MB
    GTEX-ZYFG-2026-SM-5E43Y GTEX-ZYFG 2 60-69 0 1 7.9 Small Intestine Small Intestine - Terminal Ileum 1211 124 co
    369 MB
    GTEX-ZYWO-1526-SM-5SIAL GTEX-ZYWO 2 40-49 0 0 7.2 Small Intestine Small Intestine - Terminal Ileum 1211 134 co
    369 MB
    GTEX-ZZ64-0526-SM-5GZXM GTEX-ZZ64 1 20-29 0 0 7.7 Small Intestine Small Intestine - Terminal Ileum 1211 162 co
    369 MB
    Contact

    Department of Biostatistics
    Harvard T.H. Chan School of Public Health

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