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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 Liver PANDA netZooM 0.1
    coR
    Motif TF 644 30243 137 D
    2 Liver PANDA-LIONESS netZooM 0.1
    coR
    Motif TF 644 30243 137 D
    3 Liver PUMA netZooM 0.3
    coR
    - miRanda miRNA 643 16161 137 D
    4 Liver PUMA netZooM 0.3
    coR
    - TargetScan miRNA 643 16161 137 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
    45 GB
    GTEX-1192X-1026-SM-5H12P GTEX-1192X 1 50-59 4 1 6 Liver Liver 1114 889 co
    369 MB
    GTEX-11DXY-0526-SM-5EGGQ GTEX-11DXY 1 60-69 2 1 6.8 Liver Liver 1114 891 co
    369 MB
    GTEX-11DXZ-0126-SM-5EGGY GTEX-11DXZ 1 50-59 0 1 7.9 Liver Liver 1114 250 co
    369 MB
    GTEX-11EQ9-0526-SM-5A5JZ GTEX-11EQ9 1 30-39 2 1 8.1 Liver Liver 1114 82 co
    369 MB
    GTEX-11GSP-0626-SM-5986T GTEX-11GSP 2 60-69 2 1 6.2 Liver Liver 1114 771 co
    369 MB
    GTEX-11NUK-1226-SM-5P9GM GTEX-11NUK 1 50-59 2 1 6.1 Liver Liver 1114 956 co
    369 MB
    GTEX-11NV4-1326-SM-5HL6V GTEX-11NV4 1 60-69 2 1 5.9 Liver Liver 1114 1152 co
    369 MB
    GTEX-11OF3-0726-SM-5BC4Z GTEX-11OF3 1 60-69 2 2 6 Liver Liver 1114 790 co
    369 MB
    GTEX-11TT1-1726-SM-5EQLJ GTEX-11TT1 1 20-29 0 1 9.1 Liver Liver 1114 98 co
    369 MB
    GTEX-11TUW-1726-SM-5BC5C GTEX-11TUW 1 60-69 2 2 6.1 Liver Liver 1114 755 co
    369 MB
    GTEX-11UD2-1626-SM-5EQM3 GTEX-11UD2 1 50-59 2 1 5.8 Liver Liver 1114 945 co
    369 MB
    GTEX-11WQC-0726-SM-5EQMR GTEX-11WQC 1 60-69 2 1 6.6 Liver Liver 1114 696 co
    369 MB
    GTEX-11ZTS-1426-SM-5EQMM GTEX-11ZTS 2 60-69 2 1 6.1 Liver Liver 1114 659 co
    369 MB
    GTEX-11ZUS-2526-SM-59872 GTEX-11ZUS 1 30-39 1 2 6.7 Liver Liver 1114 1426 co
    369 MB
    GTEX-11ZVC-0726-SM-5FQT9 GTEX-11ZVC 2 50-59 2 1 6.2 Liver Liver 1114 541 co
    369 MB
    GTEX-1212Z-0226-SM-59HLF GTEX-1212Z 1 60-69 2 1 6.4 Liver Liver 1114 604 co
    369 MB
    GTEX-12696-0826-SM-5EGGE GTEX-12696 1 60-69 3 1 7 Liver Liver 1114 519 co
    369 MB
    GTEX-1269C-0626-SM-5FQSS GTEX-1269C 2 60-69 2 2 6.2 Liver Liver 1114 794 co
    369 MB
    GTEX-12KS4-1326-SM-5LUB3 GTEX-12KS4 1 30-39 0 1 6 Liver Liver 1114 500 co
    369 MB
    GTEX-12WSD-1426-SM-5GCN9 GTEX-12WSD 2 60-69 2 1 6.9 Liver Liver 1114 527 co
    369 MB
    GTEX-12WSG-0626-SM-5FQTQ GTEX-12WSG 2 50-59 0 1 6.6 Liver Liver 1114 338 co
    369 MB
    GTEX-12WSI-0226-SM-5GCNA GTEX-12WSI 1 50-59 2 1 5.8 Liver Liver 1114 744 co
    369 MB
    GTEX-12WSL-0226-SM-5CVMJ GTEX-12WSL 1 50-59 0 1 6.7 Liver Liver 1114 209 co
    369 MB
    GTEX-12WSM-0726-SM-5GCOW GTEX-12WSM 1 60-69 2 1 5.9 Liver Liver 1114 971 co
    369 MB
    GTEX-12ZZZ-1326-SM-59HKW GTEX-12ZZZ 1 60-69 2 1 5.8 Liver Liver 1114 857 co
    369 MB
    GTEX-13112-1426-SM-5EGH8 GTEX-13112 1 50-59 2 1 5.7 Liver Liver 1114 1234 co
    369 MB
    GTEX-13113-1326-SM-5GCOI GTEX-13113 2 60-69 0 1 7 Liver Liver 1114 254 co
    369 MB
    GTEX-131XE-0326-SM-5LZVO GTEX-131XE 1 50-59 0 1 6.3 Liver Liver 1114 173 co
    369 MB
    GTEX-131XH-0626-SM-5LZWH GTEX-131XH 1 50-59 2 1 6.5 Liver Liver 1114 1109 co
    369 MB
    GTEX-131YS-1626-SM-5HL6C GTEX-131YS 2 60-69 2 1 6 Liver Liver 1114 997 co
    369 MB
    GTEX-132AR-0426-SM-5IFH8 GTEX-132AR 2 50-59 0 1 6.8 Liver Liver 1114 86 co
    369 MB
    GTEX-132NY-0926-SM-5P9G3 GTEX-132NY 1 60-69 1 1 7.4 Liver Liver 1114 576 co
    369 MB
    GTEX-1399R-1226-SM-5P9GF GTEX-1399R 1 30-39 0 1 8.6 Liver Liver 1114 122 co
    369 MB
    GTEX-1399T-0826-SM-5IFES GTEX-1399T 1 60-69 2 1 6.2 Liver Liver 1114 771 co
    369 MB
    GTEX-139TS-1426-SM-5IFJD GTEX-139TS 1 60-69 2 1 6.2 Liver Liver 1114 1181 co
    369 MB
    GTEX-139TU-0826-SM-5IJFG GTEX-139TU 1 60-69 3 1 6.2 Liver Liver 1114 568 co
    369 MB
    GTEX-139UC-1426-SM-5IJGH GTEX-139UC 1 60-69 2 1 6.4 Liver Liver 1114 724 co
    369 MB
    GTEX-139YR-0226-SM-5IFEM GTEX-139YR 1 50-59 0 1 5.9 Liver Liver 1114 162 co
    369 MB
    GTEX-13FLV-0326-SM-5N9DJ GTEX-13FLV 1 50-59 2 1 5.7 Liver Liver 1114 1045 co
    369 MB
    GTEX-13FTW-1126-SM-5J2NV GTEX-13FTW 1 40-49 0 1 7.7 Liver Liver 1114 163 co
    369 MB
    GTEX-13FTZ-0726-SM-5IFFY GTEX-13FTZ 1 60-69 2 2 5.8 Liver Liver 1114 1026 co
    369 MB
    GTEX-13N11-0926-SM-5IJG2 GTEX-13N11 2 50-59 0 0 8.8 Liver Liver 1114 170 co
    369 MB
    GTEX-13N2G-0926-SM-5IFGJ GTEX-13N2G 1 60-69 2 1 6 Liver Liver 1114 534 co
    369 MB
    GTEX-13NYB-1026-SM-5IFH3 GTEX-13NYB 1 40-49 2 1 6.1 Liver Liver 1114 1034 co
    369 MB
    GTEX-13NZ9-1326-SM-5MR3V GTEX-13NZ9 1 50-59 0 1 5.7 Liver Liver 1114 472 co
    369 MB
    GTEX-13NZB-0626-SM-5IFH6 GTEX-13NZB 1 30-39 1 1 5.9 Liver Liver 1114 323 co
    369 MB
    GTEX-13O1R-2026-SM-5KM3N GTEX-13O1R 1 60-69 2 1 6.6 Liver Liver 1114 855 co
    369 MB
    GTEX-13O3O-1826-SM-5IFGW GTEX-13O3O 2 60-69 3 2 6.5 Liver Liver 1114 857 co
    369 MB
    GTEX-13OVJ-1026-SM-5IFGI GTEX-13OVJ 2 50-59 2 1 6.2 Liver Liver 1114 1129 co
    369 MB
    GTEX-13OW6-2626-SM-5IFF2 GTEX-13OW6 1 50-59 2 2 6.8 Liver Liver 1114 643 co
    369 MB
    GTEX-13PVQ-1526-SM-5IFEQ GTEX-13PVQ 1 50-59 2 1 6.2 Liver Liver 1114 913 co
    369 MB
    GTEX-13PVR-0126-SM-5S2PY GTEX-13PVR 2 60-69 0 1 8.7 Liver Liver 1114 106 co
    369 MB
    GTEX-13QJC-0726-SM-5RQJK GTEX-13QJC 2 60-69 2 2 6.7 Liver Liver 1114 1063 co
    369 MB
    GTEX-13SLX-1226-SM-5S2Q6 GTEX-13SLX 2 50-59 2 1 6.1 Liver Liver 1114 1101 co
    369 MB
    GTEX-13VXU-0926-SM-5IFFH GTEX-13VXU 1 50-59 2 1 6.1 Liver Liver 1114 978 co
    369 MB
    GTEX-144GM-1326-SM-5LU5E GTEX-144GM 1 20-29 0 1 7.3 Liver Liver 1114 265 co
    369 MB
    GTEX-145LU-1326-SM-5LU9N GTEX-145LU 1 50-59 2 1 5.8 Liver Liver 1114 1033 co
    369 MB
    GTEX-145MF-0826-SM-5QGQA GTEX-145MF 1 50-59 2 1 6.4 Liver Liver 1114 955 co
    369 MB
    GTEX-145MO-2326-SM-5NQ9K GTEX-145MO 1 60-69 3 1 6.8 Liver Liver 1114 698 co
    369 MB
    GTEX-146FH-1526-SM-5NQBU GTEX-146FH 2 50-59 0 1 8.3 Liver Liver 1114 471 co
    369 MB
    GTEX-14753-1626-SM-5NQ9L GTEX-14753 1 60-69 4 1 6.6 Liver Liver 1114 893 co
    369 MB
    GTEX-147F4-1426-SM-5LUA8 GTEX-147F4 1 50-59 2 1 7 Liver Liver 1114 1268 co
    369 MB
    GTEX-147JS-1126-SM-5RQIW GTEX-147JS 1 60-69 2 1 6.2 Liver Liver 1114 547 co
    369 MB
    GTEX-1497J-0726-SM-5Q5D1 GTEX-1497J 1 60-69 0 1 6.3 Liver Liver 1114 238 co
    369 MB
    GTEX-14A5I-1726-SM-5QGQ5 GTEX-14A5I 2 50-59 4 1 6.7 Liver Liver 1114 918 co
    369 MB
    GTEX-14AS3-0126-SM-5Q5F4 GTEX-14AS3 2 40-49 0 0 6.8 Liver Liver 1114 98 co
    369 MB
    GTEX-14C38-1526-SM-5RQJ7 GTEX-14C38 1 50-59 0 1 6.3 Liver Liver 1114 584 co
    369 MB
    GTEX-14DAQ-1726-SM-5S2R2 GTEX-14DAQ 2 60-69 4 1 6.1 Liver Liver 1114 503 co
    369 MB
    GTEX-14E1K-0326-SM-5S2PE GTEX-14E1K 1 50-59 0 1 6.8 Liver Liver 1114 172 co
    369 MB
    GTEX-O5YT-0826-SM-3TW8N GTEX-O5YT 1 20-29 0 0 7.4 Liver Liver 1114 168 co
    369 MB
    GTEX-OOBJ-0826-SM-3NB2K GTEX-OOBJ 1 60-69 0 1 7.2 Liver Liver 1114 139 co
    369 MB
    GTEX-P44G-1126-SM-3NM9D GTEX-P44G 1 30-39 0 1 6 Liver Liver 1114 722 co
    369 MB
    GTEX-P78B-1326-SM-3P611 GTEX-P78B 2 40-49 1 7.8 Liver Liver 1114 573 co
    369 MB
    GTEX-PWOO-0826-SM-48TCL GTEX-PWOO 2 40-49 0 1 7.8 Liver Liver 1114 178 co
    369 MB
    GTEX-PX3G-0826-SM-48TZS GTEX-PX3G 2 20-29 0 1 7.5 Liver Liver 1114 222 co
    369 MB
    GTEX-Q2AG-1126-SM-48U1P GTEX-Q2AG 2 40-49 2 1 6.2 Liver Liver 1114 807 co
    369 MB
    GTEX-Q734-0326-SM-48U15 GTEX-Q734 2 40-49 0 1 8.7 Liver Liver 1114 45 co
    369 MB
    GTEX-QDVN-0826-SM-48TZ2 GTEX-QDVN 1 50-59 0 1 8.8 Liver Liver 1114 152 co
    369 MB
    GTEX-QEG4-1826-SM-4R1JN GTEX-QEG4 1 30-39 1 2 7.4 Liver Liver 1114 970 co
    369 MB
    GTEX-QEL4-1226-SM-447A4 GTEX-QEL4 1 50-59 3 1 7.9 Liver Liver 1114 532 co
    369 MB
    GTEX-QESD-2026-SM-447BI GTEX-QESD 1 20-29 0 1 7.4 Liver Liver 1114 367 co
    369 MB
    GTEX-QV44-0326-SM-4R1KD GTEX-QV44 1 50-59 0 1 8.5 Liver Liver 1114 83 co
    369 MB
    GTEX-R53T-0326-SM-48FEC GTEX-R53T 2 50-59 0 1 9.4 Liver Liver 1114 69 co
    369 MB
    GTEX-REY6-1226-SM-48FDR GTEX-REY6 1 60-69 0 1 6.2 Liver Liver 1114 304 co
    369 MB
    GTEX-RM2N-1926-SM-48FCU GTEX-RM2N 1 50-59 0 0 8.9 Liver Liver 1114 505 co
    369 MB
    GTEX-RN64-1826-SM-48FDV GTEX-RN64 1 50-59 1 1 6.4 Liver Liver 1114 784 co
    369 MB
    GTEX-RNOR-1426-SM-48FDJ GTEX-RNOR 2 50-59 1 1 6.2 Liver Liver 1114 940 co
    369 MB
    GTEX-RTLS-1326-SM-46MUN GTEX-RTLS 2 60-69 4 1 6.6 Liver Liver 1114 668 co
    369 MB
    GTEX-RU72-1426-SM-46MUF GTEX-RU72 2 50-59 2 1 6.2 Liver Liver 1114 502 co
    369 MB
    GTEX-RWSA-1426-SM-47JXA GTEX-RWSA 1 40-49 1 1 6.4 Liver Liver 1114 1361 co
    369 MB
    GTEX-S32W-1926-SM-4AD63 GTEX-S32W 2 50-59 0 1 7.3 Liver Liver 1114 363 co
    369 MB
    GTEX-S33H-1626-SM-4AD68 GTEX-S33H 1 30-39 2 1 6.6 Liver Liver 1114 248 co
    369 MB
    GTEX-S4Z8-0526-SM-4AD4T GTEX-S4Z8 1 60-69 0 1 8.7 Liver Liver 1114 127 co
    369 MB
    GTEX-SJXC-1226-SM-4DM78 GTEX-SJXC 1 60-69 2 2 6 Liver Liver 1114 1060 co
    369 MB
    GTEX-T6MN-1226-SM-3NMA5 GTEX-T6MN 1 50-59 2 1 6.7 Liver Liver 1114 832 co
    369 MB
    GTEX-TKQ2-1726-SM-4DXUP GTEX-TKQ2 1 50-59 0 1 8.4 Liver Liver 1114 235 co
    369 MB
    GTEX-U3ZN-0226-SM-3DB8D GTEX-U3ZN 2 30-39 0 1 9.1 Liver Liver 1114 114 co
    369 MB
    GTEX-U8XE-1526-SM-4E3HT GTEX-U8XE 1 30-39 4 1 7.8 Liver Liver 1114 418 co
    369 MB
    GTEX-UPIC-0926-SM-4IHLV GTEX-UPIC 2 20-29 0 1 6.7 Liver Liver 1114 226 co
    369 MB
    GTEX-UPK5-1426-SM-4JBHH GTEX-UPK5 1 40-49 0 1 7.3 Liver Liver 1114 1001 co
    369 MB
    GTEX-UTHO-2426-SM-4JBHD GTEX-UTHO 1 60-69 3 2 9.3 Liver Liver 1114 489 co
    369 MB
    GTEX-VUSG-0126-SM-4KL1X GTEX-VUSG 1 50-59 0 1 8.2 Liver Liver 1114 128 co
    369 MB
    GTEX-WFON-1726-SM-4LVMQ GTEX-WFON 1 40-49 0 1 8 Liver Liver 1114 238 co
    369 MB
    GTEX-WK11-1326-SM-4OOSI GTEX-WK11 1 50-59 1 2 6.4 Liver Liver 1114 943 co
    369 MB
    GTEX-WQUQ-1926-SM-4OOSA GTEX-WQUQ 1 60-69 0 1 6.7 Liver Liver 1114 494 co
    369 MB
    GTEX-WY7C-0726-SM-4ONCB GTEX-WY7C 1 50-59 0 1 9.5 Liver Liver 1114 180 co
    369 MB
    GTEX-WYVS-1926-SM-4PQZ2 GTEX-WYVS 2 40-49 0 1 8.2 Liver Liver 1114 297 co
    369 MB
    GTEX-WYVS-1926-SM-4SOIC GTEX-WYVS 2 40-49 0 1 8.2 Liver Liver 1114 297 co
    369 MB
    GTEX-WZTO-0626-SM-4PQYY GTEX-WZTO 1 40-49 1 1 7.4 Liver Liver 1114 499 co
    369 MB
    GTEX-X261-1726-SM-4PQYT GTEX-X261 1 50-59 4 1 5.8 Liver Liver 1114 858 co
    369 MB
    GTEX-X3Y1-2726-SM-4PQZH GTEX-X3Y1 1 40-49 0 1 8.1 Liver Liver 1114 214 co
    369 MB
    GTEX-X4EO-1126-SM-4QARQ GTEX-X4EO 2 60-69 3 1 7.1 Liver Liver 1114 804 co
    369 MB
    GTEX-X4EP-1026-SM-4QAS5 GTEX-X4EP 2 60-69 4 2 6.7 Liver Liver 1114 1137 co
    369 MB
    GTEX-X4XY-1626-SM-46MVN GTEX-X4XY 1 60-69 0 1 6.7 Liver Liver 1114 653 co
    369 MB
    GTEX-XBEC-1526-SM-4AT68 GTEX-XBEC 1 50-59 2 2 6.3 Liver Liver 1114 536 co
    369 MB
    GTEX-XOTO-0826-SM-4B65O GTEX-XOTO 1 50-59 2 1 7.3 Liver Liver 1114 658 co
    369 MB
    GTEX-XXEK-1126-SM-4BRUX GTEX-XXEK 1 50-59 0 1 8.7 Liver Liver 1114 169 co
    369 MB
    GTEX-Y5LM-0426-SM-4VBRO GTEX-Y5LM 2 40-49 0 1 9.8 Liver Liver 1114 83 co
    369 MB
    GTEX-Y5V5-0926-SM-4VBPZ GTEX-Y5V5 2 60-69 0 1 7 Liver Liver 1114 188 co
    369 MB
    GTEX-YB5E-0326-SM-5IFHU GTEX-YB5E 1 40-49 0 1 8.3 Liver Liver 1114 163 co
    369 MB
    GTEX-YEC4-0826-SM-5P9FV GTEX-YEC4 1 40-49 0 1 7.4 Liver Liver 1114 198 co
    369 MB
    GTEX-YECK-1926-SM-4W21H GTEX-YECK 1 60-69 3 2 6.4 Liver Liver 1114 608 co
    369 MB
    GTEX-YFC4-1526-SM-5IFJS GTEX-YFC4 2 40-49 1 2 6 Liver Liver 1114 772 co
    369 MB
    GTEX-Z9EW-0426-SM-5CVM9 GTEX-Z9EW 1 40-49 0 1 7.2 Liver Liver 1114 202 co
    369 MB
    GTEX-ZAB4-0826-SM-5LU9D GTEX-ZAB4 1 40-49 4 2 5.7 Liver Liver 1114 503 co
    369 MB
    GTEX-ZAB5-0426-SM-5CVMI GTEX-ZAB5 1 50-59 0 0 7.8 Liver Liver 1114 177 co
    369 MB
    GTEX-ZEX8-0826-SM-4WKHK GTEX-ZEX8 1 50-59 0 1 7.8 Liver Liver 1114 85 co
    369 MB
    GTEX-ZF29-2026-SM-4WWB7 GTEX-ZF29 2 60-69 0 0 9.1 Liver Liver 1114 164 co
    369 MB
    GTEX-ZF2S-3026-SM-4WWCH GTEX-ZF2S 2 50-59 0 1 9.5 Liver Liver 1114 89 co
    369 MB
    GTEX-ZPU1-0826-SM-57WG2 GTEX-ZPU1 1 40-49 0 0 9.6 Liver Liver 1114 103 co
    369 MB
    GTEX-ZTPG-1426-SM-51MT3 GTEX-ZTPG 2 20-29 0 2 6.8 Liver Liver 1114 254 co
    369 MB
    GTEX-ZVP2-0626-SM-51MSO GTEX-ZVP2 1 50-59 0 0 7.7 Liver Liver 1114 137 co
    369 MB
    GTEX-ZVT3-1626-SM-5GU66 GTEX-ZVT3 2 60-69 2 1 6 Liver Liver 1114 623 co
    369 MB
    GTEX-ZVT4-0626-SM-5E45T GTEX-ZVT4 2 50-59 3 1 5.9 Liver Liver 1114 615 co
    369 MB
    GTEX-ZYT6-0626-SM-5E45V GTEX-ZYT6 1 30-39 1 2 6.6 Liver Liver 1114 1412 co
    369 MB
    GTEX-ZYY3-0626-SM-5NQ6W GTEX-ZYY3 2 60-69 4 1 5.7 Liver Liver 1114 497 co
    369 MB
    GTEX-ZZPU-0426-SM-5GZYH GTEX-ZZPU 2 50-59 0 1 7.8 Liver Liver 1114 192 co
    369 MB
    Contact

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

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