DOCSLIB.ORG

Supplementary File S4. Genes Within Each Module Mackay Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary File S4. Genes Within Each Module Mackay Et Al Supplementary File S4. Genes within each module Mackay et al. coefficient Entrez_Gene_ID Symbol Probe_Id ESR1.1 -1 991 CDC20 ILMN_1663390 -1 1476 CSTB ILMN_1761797 -1 1503 CTPS ILMN_1783285 1 3708 ITPR1 ILMN_1789505 -1 4281 MID1 ILMN_1761858 -1 4781 NFIB ILMN_1778991 -1 5433 POLR2D ILMN_1792672 1 5684 PSMA3 ILMN_1694931 -1 6317 SERPINB3 ILMN_1703855 -1 6446 SGK ILMN_1702487 -1 7159 TP53BP2 ILMN_1779706 1 7251 TSG101 ILMN_1747146 -1 8208 CHAF1B ILMN_1674231 -1 8543 LMO4 ILMN_1703487 -1 9353 SLIT2 ILMN_1676449 -1 10200 MPHOSPH6 ILMN_1746682 -1 10982 MAPRE2 ILMN_1695276 -1 25925 ZNF521 ILMN_1679747 -1 27436 EML4 ILMN_1718297 1 55970 GNG12 ILMN_1673380 1 56204 KIAA1370 ILMN_1700733 1 56890 MDM1 ILMN_1750703 -1 56942 C16orf61 ILMN_1783333 -1 58528 RRAGD ILMN_1699772 1 5825 ABCD3 ILMN_1674032 1 36 ACADSB ILMN_1740920 -1 92 ACVR2A ILMN_1670912 -1 8038 ADAM12 ILMN_1705689 -1 60312 AFAP ILMN_1701998 1 3899 AFF3 ILMN_1775235 1 10551 AGR2 ILMN_1814151 -1 55966 AJAP1 ILMN_1723521 -1 122481 AK7 ILMN_1684305 1 11215 AKAP11 ILMN_1693220 1 9068 ANGPTL1 ILMN_1669773 -1 26057 ANKRD17 ILMN_1712019 -1 163782 ANKRD38 ILMN_1776936 1 10053 AP1M2 ILMN_1705861 1 63941 APBA2BP ILMN_1749738 -1 147495 APCDD1 ILMN_1656951 1 51074 APIP ILMN_1793598 1 367 AR ILMN_1767351 1 9828 ARHGEF17 ILMN_1754562 1 403 ARL3 ILMN_1780444 1 9915 ARNT2 ILMN_1718046 1 22901 ARSG ILMN_1720604 -1 419 ART3 ILMN_1693218 1 427 ASAH1 ILMN_1684054 -1 84002 B3GNT5 ILMN_1702609 -1 25825 BACE2 ILMN_1669323 -1 11176 BAZ2A ILMN_1676318 -1 8424 BBOX1 ILMN_1734929 -1 637 BID ILMN_1763386 1 8548 BLZF1 ILMN_1669140 -1 25798 BRI3 ILMN_1781580 1 8945 BTRC ILMN_1815718 -1 221061 FAM171A1 ILMN_1749868 1 84229 CCDC135 ILMN_1712067 1 80169 C17orf68 ILMN_1755711 -1 29919 C18orf8 ILMN_1719097 1 81563 C1orf21 ILMN_1797735 -1 114897 C1QTNF1 ILMN_1694608 1 55614 KIF16B ILMN_1772786 -1 140862 C20orf82 ILMN_1772869 1 79669 C3orf52 ILMN_1672969 1 79624 C6orf211 ILMN_1798108 1 80129 C6orf97 ILMN_1772588 -1 761 CA3 ILMN_1740996 -1 794 CALB2 ILMN_1748840 1 842 CASP9 ILMN_1718070 1 51019 CCDC53 ILMN_1715569 -1 6362 CCL18 ILMN_1654411 1 1026 CDKN1A ILMN_1784602 1 84181 CHD6 ILMN_1781816 1 1124 CHN2 ILMN_1774110 -1 9435 CHST2 ILMN_1794011 1 64084 CLSTN2 ILMN_1731237 1 1191 CLU ILMN_1724895 -1 112616 CMTM7 ILMN_1698934 -1 169044 COL22A1 ILMN_1784532 -1 51692 CPSF3 ILMN_1808458 -1 64764 CREB3L2 ILMN_1751097 1 1387 CREBBP ILMN_1809583 1 1396 CRIP1 ILMN_1742350 -1 8531 CSDA ILMN_1782788 -1 1439 CSF2RB ILMN_1798475 -1 1466 CSRP2 ILMN_1660806 1 8722 CTSF ILMN_1750122 -1 1521 CTSW ILMN_1794364 -1 55917 CTTNBP2NL ILMN_1719517 -1 10659 CUGBP2 ILMN_1668652 -1 6387 CXCL12 ILMN_1791447 1 90736 FAM104B ILMN_1705848 -1 10046 CXorf6 ILMN_1680856 1 124637 CYB5D1 ILMN_1670925 1 51706 CYB5R1 ILMN_1729237 -1 1612 DAPK1 ILMN_1708340 1 51164 DCTN4 ILMN_1741564 -1 23586 DDX58 ILMN_1797001 1 26063 DECR2 ILMN_1783337 -1 163259 DENND2C ILMN_1815035 1 51635 DHRS7 ILMN_1807455 1 1741 DLG3 ILMN_1811515 1 56521 DNAJC12 ILMN_1803073 1 7802 DNALI1 ILMN_1745501 -1 26010 DNAPTP6 ILMN_1683678 -1 1788 DNMT3A ILMN_1676128 -1 1807 DPYS ILMN_1749324 -1 1824 DSC2 ILMN_1782125 -1 1827 RCAN1 ILMN_1814135 -1 1830 DSG3 ILMN_1655468 -1 56940 DUSP22 ILMN_1801331 -1 1870 E2F2 ILMN_1777233 -1 1871 E2F3 ILMN_1652143 -1 1906 EDN1 ILMN_1682775 -1 1956 EGFR ILMN_1798975 1 1964 EIF1AX ILMN_1808344 -1 9470 EIF4E2 ILMN_1738326 -1 2001 ELF5 ILMN_1813270 1 60481 ELOVL5 ILMN_1712533 -1 2019 EN1 ILMN_1709593 1 955 ENTPD6 ILMN_1677955 1 2046 EPHA8 ILMN_1756989 -1 2064 ERBB2 ILMN_1694303 1 2099 ESR1 ILMN_1678535 -1 10205 MPZL2 ILMN_1752932 -1 2131 EXT1 ILMN_1794343 -1 2173 FABP7 ILMN_1804948 -1 57488 FAM62B ILMN_1807761 -1 2195 FAT ILMN_1754795 -1 2199 FBLN2 ILMN_1774602 1 2203 FBP1 ILMN_1728799 -1 114907 FBXO32 ILMN_1703955 1 2263 FGFR2 ILMN_1682270 1 163486 DENND1B ILMN_1763654 1 55638 FLJ20366 ILMN_1738989 -1 79919 FLJ22671 ILMN_1665471 -1 153830 RNF145 ILMN_1719951 1 132720 C4orf32 ILMN_1700257 -1 151195 CCNYL1 ILMN_1810069 -1 346689 FLJ44186 ILMN_1807691 1 2321 FLT1 ILMN_1705002 1 2330 FMO5 ILMN_1811632 -1 84624 FNDC1 ILMN_1734653 1 3169 FOXA1 ILMN_1766650 -1 2295 FOXF2 ILMN_1683960 -1 53826 FXYD6 ILMN_1768812 -1 2533 FYB ILMN_1796537 -1 2564 GABRE ILMN_1784706 1 2593 GAMT ILMN_1794595 1 2625 GATA3 ILMN_1727652 -1 115361 GBP4 ILMN_1771385 -1 2707 GJB3 ILMN_1652390 -1 2709 GJB5 ILMN_1735365 1 26035 GLCE ILMN_1714349 -1 2719 GPC3 ILMN_1799759 1 23171 GPD1L ILMN_1694106 1 2850 GPR27 ILMN_1744034 1 27198 GPR81 ILMN_1811272 -1 51704 GPRC5B ILMN_1786034 -1 63940 GPSM3 ILMN_1662799 -1 2886 GRB7 ILMN_1740762 1 79774 GRTP1 ILMN_1745068 1 51440 HPCAL4 ILMN_1736976 -1 3294 HSD17B2 ILMN_1808713 -1 3455 IFNAR2 ILMN_1791057 1 3480 IGF1R ILMN_1721653 -1 3600 IL15 ILMN_1724181 -1 3559 IL2RA ILMN_1683774 -1 9235 IL32 ILMN_1778010 -1 10527 IPO7 ILMN_1682647 -1 79192 IRX1 ILMN_1735353 1 10265 IRX5 ILMN_1757736 -1 3680 ITGA9 ILMN_1813117 -1 3689 ITGB2 ILMN_1654396 1 3712 IVD ILMN_1724207 1 126823 KLHDC9 ILMN_1701918 -1 3783 KCNN4 ILMN_1726320 1 200845 KCTD6 ILMN_1800942 -1 11015 KDELR3 ILMN_1722820 1 9812 KIAA0141 ILMN_1762990 -1 9914 KIAA0703 ILMN_1785413 1 57148 KIAA1219 ILMN_1733115 1 26128 KIAA1279 ILMN_1745813 1 57535 KIAA1324 ILMN_1771482 1 222223 KIAA1324L ILMN_1652371 -1 55582 KIF27 ILMN_1692572 1 11127 KIF3A ILMN_1653385 -1 3801 KIFC3 ILMN_1715900 -1 51621 KLF13 ILMN_1679929 -1 688 KLF5 ILMN_1770293 -1 5655 KLK10 ILMN_1688205 -1 25818 KLK5 ILMN_1718731 -1 5653 KLK6 ILMN_1780255 -1 5650 KLK7 ILMN_1745570 -1 3872 KRT17 ILMN_1666845 -1 25984 KRT23 ILMN_1791545 -1 3852 KRT5 ILMN_1801632 -1 3854 KRT6B ILMN_1721354 -1 8942 KYNU ILMN_1746517 -1 27074 LAMP3 ILMN_1719734 -1 93273 LEMD1 ILMN_1785444 1 80774 LIMD2 ILMN_1673867 -1 3985 LIMK2 ILMN_1660624 1 89782 LMLN ILMN_1815716 -1 197135 LOC197135 ILMN_1803596 -1 57228 LOC57228 ILMN_1804415 1 90355 C5orf30 ILMN_1677292 -1 84171 LOXL4 ILMN_1754174 1 987 LRBA ILMN_1652160 1 26018 LRIG1 ILMN_1707342 1 90506 LRRC46 ILMN_1768818 -1 56262 LRRC8A ILMN_1739840 -1 84230 LRRC8C ILMN_1765855 1 4049 LTA ILMN_1666732 1 10916 MAGED2 ILMN_1683576 -1 84441 MAML2 ILMN_1765729 1 9053 MAP7 ILMN_1712719 1 4137 MAPT ILMN_1710903 1 375449 LOC375449 ILMN_1738438 1 92014 MCART1 ILMN_1772492 -1 51102 MECR ILMN_1683160 -1 4240 MFGE8 ILMN_1756071 -1 6157 RPL27A ILMN_1716740 1 79083 MLPH ILMN_1795342 -1 4322 MMP13 ILMN_1771030 -1 4316 MMP7 ILMN_1685403 1 51073 MRPL4 ILMN_1804207 1 10884 MRPS30 ILMN_1726743 1 4604 MYBPC1 ILMN_1752075 -1 4643 MYO1E ILMN_1773342 1 9 NAT1 ILMN_1688071 1 115677 NOSTRIN ILMN_1783665 -1 4860 NP ILMN_1777534 -1 8828 NRP2 ILMN_1787190 1 9369 NRXN3 ILMN_1720935 -1 79902 NUP85 ILMN_1669635 1 78990 OTUB2 ILMN_1799198 -1 286530 P2RY8 ILMN_1768284 -1 11240 PADI2 ILMN_1771223 1 56924 PAK6 ILMN_1708223 1 56288 PARD3 ILMN_1710524 1 5092 PCBD1 ILMN_1795906 1 54039 PCBP3 ILMN_1687216 1 648 BMI1 ILMN_1700915 1 5046 PCSK6 ILMN_1802550 -1 5156 PDGFRA ILMN_1681949 1 27152 INTU ILMN_1716564 1 5570 PKIB ILMN_1768268 1 5327 PLAT ILMN_1738742 -1 5337 PLD1 ILMN_1719696 -1 5341 PLEK ILMN_1795762 -1 57480 PLEKHG1 ILMN_1805606 -1 5351 PLOD1 ILMN_1684391 1 5357 PLS1 ILMN_1759206 1 25885 POLR1A ILMN_1780758 -1 10891 PPARGC1A ILMN_1750062 -1 5475 PPEF1 ILMN_1652017 1 5509 PPP1R3D ILMN_1781198 1 5521 PPP2R2B ILMN_1660732 -1 639 PRDM1 ILMN_1655077 -1 5549 PRELP ILMN_1707380 1 57580 PREX1 ILMN_1777342 -1 8842 PROM1 ILMN_1786720 -1 23362 PSD3 ILMN_1717477 -1 140885 PTPNS1 ILMN_1758146 1 5860 QDPR ILMN_1672443 1 9135 RABEP1 ILMN_1719622 -1 5918 RARRES1 ILMN_1800091 -1 83937 RASSF4 ILMN_1690566 -1 6091 ROBO1 ILMN_1806790 -1 54763 ROPN1 ILMN_1668766 1 55086 CXorf57 ILMN_1703279 1 6123 RPL3L ILMN_1775175 1 9252 RPS6KA5 ILMN_1657515 -1 6251 RSU1 ILMN_1721657 -1 6273 S100A2 ILMN_1725852 -1 6279 S100A8 ILMN_1729801 -1 6304 SATB1 ILMN_1690646 1 51097 SCCPDH ILMN_1795839 1 57758 SCUBE2 ILMN_1684085 1 7869 SEMA3B ILMN_1653501 1 6405 SEMA3F ILMN_1761540 -1 123228 SENP8 ILMN_1767690 -1 23157 Sep-06 ILMN_1661342 -1 10801 Sep-09 ILMN_1769118 -1 5271 SERPINB8 ILMN_1718960 -1 5270 SERPINE2 ILMN_1655595 1 29946 SERTAD3 ILMN_1801934 1 389376 SFTPG ILMN_1703864 -1 399694 SHC4 ILMN_1807050 -1 55423 SIRPB2 ILMN_1771801 -1 56833 SLAMF8 ILMN_1667224 -1 6565 SLC15A2 ILMN_1706040 1 6512 SLC1A7 ILMN_1704629 1 6584 SLC22A5 ILMN_1699357 -1 60386 SLC25A19 ILMN_1666553 -1 7782 SLC30A4 ILMN_1653098 -1 10237 SLC35B1 ILMN_1727840 1 25800 SLC39A6 ILMN_1750394 -1 8884 SLC5A6 ILMN_1741054 1 6542 SLC7A2 ILMN_1781400 -1 6608 SMO ILMN_1782098 -1 64750 SMURF2 ILMN_1675429 -1 6627 SNRPA1 ILMN_1715179 1 28966 SNX24 ILMN_1795666 -1 6648 SOD2 ILMN_1775672 -1 6667 SP1 ILMN_1676010 -1 23648 SSBP3 ILMN_1814165 -1 8082 SSPN ILMN_1775486 -1 6489 ST8SIA1 ILMN_1664859 1 8614 STC2 ILMN_1691884 1 27148 STK36 ILMN_1693538 -1 23208 SYT11 ILMN_1789954 1 23158 TBC1D9 ILMN_1703891 -1 6934 TCF7L2 ILMN_1672486 -1 6999 TDO2 ILMN_1716859 1 7031 TFF1 ILMN_1722489 -1 7046 TGFBR1 ILMN_1797611 1 7057 THBS1 ILMN_1686116 1 79875 THSD4 ILMN_1746737 -1 7077 TIMP2 ILMN_1670054 1 283578 TMED8 ILMN_1676670 1 161291 TMEM30B ILMN_1752935 1 283131 TncRNA ILMN_1657920 -1 10673 TNFSF13B ILMN_1758418 -1 23321 TRIM2 ILMN_1745079 -1 23650 TRIM29 ILMN_1657766 1 142940 TRUB1 ILMN_1744574 1 27075 TSPAN13 ILMN_1669881 1 151613 TTC14 ILMN_1696757 1 54902 TTC19 ILMN_1781260 -1 57217 TTC7A ILMN_1732535 -1 10537 UBD ILMN_1678841 1 11274 USP18 ILMN_1740200 -1 51442 VGLL1 ILMN_1703146 -1 7472 WNT2 ILMN_1694011 1 7473 WNT3 ILMN_1784840 1 7490 WT1 ILMN_1802174 -1 57510 XPO5 ILMN_1759495 1 22882 ZHX2 ILMN_1792951 1 57336 ZNF287 ILMN_1693597 -1 10320 ZNFN1A1 ILMN_1676575 Symmans et al. coefficient Entrez_Gene_ID Symbol Probe_Id SET 1 27075 TSPAN13 ILMN_1669881
Load more

Recommended publications
  • Mouse Germ Line Mutations Due to Retrotransposon Insertions Liane Gagnier1, Victoria P
    Gagnier et al. Mobile DNA (2019) 10:15 https://doi.org/10.1186/s13100-019-0157-4 REVIEW Open Access Mouse germ line mutations due to retrotransposon insertions Liane Gagnier1, Victoria P. Belancio2 and Dixie L. Mager1* Abstract Transposable element (TE) insertions are responsible for a significant fraction of spontaneous germ line mutations reported in inbred mouse strains. This major contribution of TEs to the mutational landscape in mouse contrasts with the situation in human, where their relative contribution as germ line insertional mutagens is much lower. In this focussed review, we provide comprehensive lists of TE-induced mouse mutations, discuss the different TE types involved in these insertional mutations and elaborate on particularly interesting cases. We also discuss differences and similarities between the mutational role of TEs in mice and humans. Keywords: Endogenous retroviruses, Long terminal repeats, Long interspersed elements, Short interspersed elements, Germ line mutation, Inbred mice, Insertional mutagenesis, Transcriptional interference Background promoter and polyadenylation motifs and often a splice The mouse and human genomes harbor similar types of donor site [10, 11]. Sequences of full-length ERVs can TEs that have been discussed in many reviews, to which encode gag, pol and sometimes env, although groups of we refer the reader for more in depth and general infor- LTR retrotransposons with little or no retroviral hom- mation [1–9]. In general, both human and mouse con- ology also exist [6–9]. While not the subject of this re- tain ancient families of DNA transposons, none view, ERV LTRs can often act as cellular enhancers or currently active, which comprise 1–3% of these genomes promoters, creating chimeric transcripts with genes, and as well as many families or groups of retrotransposons, have been implicated in other regulatory functions [11– which have caused all the TE insertional mutations in 13].
    [Show full text]
  • Binnenwerk Cindy Postma.Indd
    CHAPTER 6 Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression Gut 2009, 58: 79-89 Beatriz Carvalho Cindy Postma Sandra Mongera Erik Hopmans Sharon Diskin Mark A. van de Wiel Wim van Criekinge Olivier Thas Anja Matthäi Miguel A. Cuesta Jochim S. Terhaar sive Droste Mike Craanen Evelin Schröck Bauke Ylstra Gerrit A. Meijer 104 | Chapter 6 Abstract Objective: This study aimed to identify the oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on mRNA expression of genes in this amplicon. Methods: Segmentation of DNA copy number changes on 20q was performed by array CGH in 34 non-progressed colorectal adenomas, 41 progressed adenomas (i.e. adenomas that present a focus of cancer) and 33 adenocarcinomas. Moreover, a robust analysis of altered expression of genes in these segments was performed by microarray analysis in 37 adenomas and 31 adenocarcinomas. Protein expression was evaluated by immunohistochemistry on tissue microarrays. Results: The genes C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5, mapping at 20q were signifi cantly overexpressed in carcinomas compared to adenomas as consequence of copy number gain of 20q. Conclusion: This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specifi c biomarkers for colorectal cancer with potential clinical applications. Putative oncogenes at chromosome 20q in colorectal carcinogenesis | 105 Introduction The majority of cancers are epithelial in origin and arise through a stepwise progression from normal cells, through dysplasia, into malignant cells that invade surrounding tissues and have metastatic potential.
    [Show full text]
  • Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis
    Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Molecular Mechanisms Involved Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis Ryan Fassnacht Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Physiology Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/2246 This Thesis is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Ryan C. Fassnacht 2010 All Rights Reserved Molecular Mechanisms Involved in the Interaction Effects of HCV and Ethanol on Liver Cirrhosis A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at Virginia Commonwealth University. by Ryan Christopher Fassnacht, B.S. Hampden Sydney University, 2005 M.S. Virginia Commonwealth University, 2010 Director: Valeria Mas, Ph.D., Associate Professor of Surgery and Pathology Division of Transplant Department of Surgery Virginia Commonwealth University Richmond, Virginia July 9, 2010 Acknowledgement The Author wishes to thank his family and close friends for their support. He would also like to thank the members of the molecular transplant team for their help and advice. This project would not have been possible with out the help of Dr. Valeria Mas and her endearing
    [Show full text]
  • Table 2. Significant
    Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S.
    [Show full text]
  • Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS
    Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen,
    [Show full text]
  • Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7
    [Show full text]
  • Synthetic Lethal Screen Demonstrates That a JAK2 Inhibitor Suppresses a BCL6 Dependent IL10RA/JAK2/STAT3 Pathway in High Grade B-Cell Lymphoma
    BCL6 suppresses an IL10RA/JAK2/STAT3 pathway Synthetic lethal screen demonstrates that a JAK2 inhibitor suppresses a BCL6 dependent IL10RA/JAK2/STAT3 pathway in high grade B-cell lymphoma. Daniel Beck1,6, Jenny Zobel3,6, Ruth Barber1,2,6, Sian Evans1, Larissa Lezina1, Rebecca L. Allchin1, Matthew Blades4, Richard Elliott5, Christopher J. Lord5, Alan Ashworth5, Andrew C.G. Porter3, Simon D. Wagner1 1Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute and, 2 Leicester Diagnostic and Drug Development (LD3) Centre, University of Leicester, Lancaster Road, Leicester LE1 7HB, UK, 3Department of Haematology, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK. 4Bioinformatics and Biostatistics Analysis Support Hub (B/BASH), University of Leicester, Lancaster Road, Leicester LE1 9HN and 5The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK. 6The first three authors contributed equally to this work Running title: BCL6 suppresses an IL10RA/JAK2/STAT3 pathway. To whom correspondence should be addressed: Simon D. Wagner, Department of Cancer Studies, Room 104, Hodgkin Building, University of Leicester, Lancaster Road, Leicester LE1 7HB, UK. Tel: 0441162525584, Fax: 0441162525616, Email: [email protected] Keywords: cancer therapy, Janus kinase (JAK), lymphocyte, lymphoma, transcription factor, B-cell lymphoma 6 (BCL-6), synthetic lethal screen. ABSTRACT which shows higher levels of IL10RA, JAK2 and We demonstrate the usefulness of synthetic lethal STAT3 but lower levels of BCL6 than GC- screening of a conditionally BCL6 deficient DLBCL and might be usefully combined with Burkitt lymphoma cell line, DG75-AB7, with a novel approaches such as inhibition of IL10RA.
    [Show full text]
  • Mutations in Pi(3,5)P2 Signaling and Neurodegeneration in Mouse and Human
    MUTATIONS IN PI(3,5)P2 SIGNALING AND NEURODEGENERATION IN MOUSE AND HUMAN by Clement Y. Chow A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Human Genetics) in The University of Michigan 2008 Doctoral Committee: Professor Miriam H. Meisler, Chair Professor Sally A. Camper Professor David Ginsburg Associate Professor David C. Kohrman Assistant Professor Geoffrey G. Murphy Clement Y. Chow 2008 To my wife, Candace For all her love and support ii ACKNOWLEDGEMENTS I would first like to thank my mentor, Miriam Meisler. She is the consummate scientist. Miriam is inquisitive and interested in a wide range of topics. This trait has taught me to always ask the right questions and be skeptical of conclusions that are not supported by data. Miriam’s unending desire to make each oral presentation perfect drove me to improve my own skills. I came to this lab without any public presentation skills, but I am now greatly improved in my presentation abilities, a skill crucial for a successful scientific career. Miriam is a perfectionist when it comes to writing and always encouraged me to do the same. I will continue to strive to perfect my writing abilities. I came to the lab wanting to positionally clone a mouse mutant. I told Miriam that I would stay in the lab if she allowed me to do so. She was supportive and excited from the beginning, allowing me to pursue a project with an unknown future. This allowed me to learn, first hand, many aspects of genetics that such a project provides.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Supplementary Material
    BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Page 1 / 45 SUPPLEMENTARY MATERIAL Appendix A1: Neuropsychological protocol. Appendix A2: Description of the four cases at the transitional stage. Table A1: Clinical status and center proportion in each batch. Table A2: Complete output from EdgeR. Table A3: List of the putative target genes. Table A4: Complete output from DIANA-miRPath v.3. Table A5: Comparison of studies investigating miRNAs from brain samples. Figure A1: Stratified nested cross-validation. Figure A2: Expression heatmap of miRNA signature. Figure A3: Bootstrapped ROC AUC scores. Figure A4: ROC AUC scores with 100 different fold splits. Figure A5: Presymptomatic subjects probability scores. Figure A6: Heatmap of the level of enrichment in KEGG pathways. Kmetzsch V, et al. J Neurol Neurosurg Psychiatry 2021; 92:485–493. doi: 10.1136/jnnp-2020-324647 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Neurol Neurosurg Psychiatry Appendix A1. Neuropsychological protocol The PREV-DEMALS cognitive evaluation included standardized neuropsychological tests to investigate all cognitive domains, and in particular frontal lobe functions. The scores were provided previously (Bertrand et al., 2018). Briefly, global cognitive efficiency was evaluated by means of Mini-Mental State Examination (MMSE) and Mattis Dementia Rating Scale (MDRS). Frontal executive functions were assessed with Frontal Assessment Battery (FAB), forward and backward digit spans, Trail Making Test part A and B (TMT-A and TMT-B), Wisconsin Card Sorting Test (WCST), and Symbol-Digit Modalities test.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8.440,393 B2 Birrer Et Al
    USOO8440393B2 (12) United States Patent (10) Patent No.: US 8.440,393 B2 Birrer et al. (45) Date of Patent: May 14, 2013 (54) PRO-ANGIOGENIC GENES IN OVARIAN OTHER PUBLICATIONS TUMORENDOTHELIAL CELL, SOLATES Boyd (The Basic Science of Oncology, 1992, McGraw-Hill, Inc., p. (75) Inventors: Michael J. Birrer, Mt. Airy, MD (US); 379). Tomas A. Bonome, Washington, DC Tockman et al. (Cancer Res., 1992, 52:2711s-2718s).* (US); Anil Sood, Pearland, TX (US); Pritzker (Clinical Chemistry, 2002, 48: 1147-1150).* Chunhua Lu, Missouri City, TX (US) Benedict et al. (J. Exp. Medicine, 2001, 193(1) 89-99).* Jiang et al. (J. Biol. Chem., 2003, 278(7) 4763-4769).* (73) Assignees: The United States of America as Matsushita et al. (FEBS Letters, 1999, vol. 443, pp. 348-352).* Represented by the Secretary of the Singh et al. (Glycobiology, 2001, vol. 11, pp. 587-592).* Department of Health and Human Abbosh et al. (Cancer Res. Jun. 1, 2006 66:5582-55.91 and Supple Services, Washington, DC (US); The mental Figs. S1-S7).* University of MD Anderson Cancer Zhai et al. (Chinese General Practice Aug. 2008, 11(8A): 1366 Center, Houston, TX (US) 1367).* Lu et al. (Cancer Res. Feb. 15, 2007, 64(4): 1757-1768).* (*) Notice: Subject to any disclaimer, the term of this Bagnato et al., “Activation of Mitogenic Signaling by Endothelin 1 in patent is extended or adjusted under 35 Ovarian Carcinoma Cells', Cancer Research, vol. 57, pp. 1306-1311, U.S.C. 154(b) by 194 days. 1997. Bouras et al., “Stanniocalcin 2 is an Estrogen-responsive Gene (21) Appl.
    [Show full text]
  • Supplementary Data
    Supplementary Fig. 1 A B Responder_Xenograft_ Responder_Xenograft_ NON- NON- Lu7336, Vehicle vs Lu7466, Vehicle vs Responder_Xenograft_ Responder_Xenograft_ Sagopilone, Welch- Sagopilone, Welch- Lu7187, Vehicle vs Lu7406, Vehicle vs Test: 638 Test: 600 Sagopilone, Welch- Sagopilone, Welch- Test: 468 Test: 482 Responder_Xenograft_ NON- Lu7860, Vehicle vs Responder_Xenograft_ Sagopilone, Welch - Lu7558, Vehicle vs Test: 605 Sagopilone, Welch- Test: 333 Supplementary Fig. 2 Supplementary Fig. 3 Supplementary Figure S1. Venn diagrams comparing probe sets regulated by Sagopilone treatment (10mg/kg for 24h) between individual models (Welsh Test ellipse p-value<0.001 or 5-fold change). A Sagopilone responder models, B Sagopilone non-responder models. Supplementary Figure S2. Pathway analysis of genes regulated by Sagopilone treatment in responder xenograft models 24h after Sagopilone treatment by GeneGo Metacore; the most significant pathway map representing cell cycle/spindle assembly and chromosome separation is shown, genes upregulated by Sagopilone treatment are marked with red thermometers. Supplementary Figure S3. GeneGo Metacore pathway analysis of genes differentially expressed between Sagopilone Responder and Non-Responder models displaying –log(p-Values) of most significant pathway maps. Supplementary Tables Supplementary Table 1. Response and activity in 22 non-small-cell lung cancer (NSCLC) xenograft models after treatment with Sagopilone and other cytotoxic agents commonly used in the management of NSCLC Tumor Model Response type
    [Show full text]