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Table S12: Genes Identified on GISTIC on the SNP-FASST2 Segmentation Algorithm

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Table S12: Genes identified on GISTIC on the SNP-FASST2 Segmentation Algorithm Gene Symbol Chromosome Start End Length STPG1 chr1 24683488 24741587 58100 NIPAL3 chr1 24742244 24799473 57230 RCAN3AS chr1 24822822 24828850 6029 RCAN3 chr1 24828840 24863510 34671 NCMAP chr1 24882566 24935818 53253 SRRM1 chr1 24969593 24999772 30180 CLIC4 chr1 25071759 25170815 99057 RUNX3 chr1 25226001 25291501 65501 SYF2 chr1 25548766 25559013 10248 C1orf63 chr1 25568739 25573985 5247 RHD chr1 25598980 25656936 57957 TMEM50A chr1 25664788 25688852 24065 RHCE chr1 25688739 25747363 58625 TMEM57 chr1 25757387 25826698 69312 LDLRAP1 chr1 25870075 25895377 25303 MAN1C1 chr1 25943958 26111258 167301 SEPN1 chr1 26126666 26144713 18048 LOC646471 chr1 26146444 26150097 3654 FAM54B chr1 26146396 26159433 13038 AUNIP chr1 26160496 26185848 25353 PAQR7 chr1 26187974 26197744 9771 STMN1 chr1 26210676 26233368 22693 MIR3917 chr1 26232852 26232945 94 PAFAH2 chr1 26286257 26324648 38392 EXTL1 chr1 26348270 26362954 14685 SLC30A2 chr1 26364513 26372604 8092 TRIM63 chr1 26377795 26394125 16331 PDIK1L chr1 26437655 26452039 14385 FAM110D chr1 26485510 26489119 3610 ZNF593 chr1 26496387 26497364 978 CNKSR1 chr1 26503980 26516375 12396 CATSPER4 chr1 26517118 26529033 11916 CEP85 chr1 26560692 26605299 44608 SH3BGRL3 chr1 26606212 26608013 1802 UBXN11 chr1 26608772 26644756 35985 CD52 chr1 26644410 26647014 2605 AIM1L chr1 26648349 26680621 32273 ZNF683 chr1 26688124 26699266 11143 LIN28A chr1 26737268 26756219 18952 DHDDS chr1 26758772 26797795 39024 HMGN2 chr1 26798901 26803133 4233 RPS6KA1 chr1 26856248 26901520 45273 MIR1976 chr1 26881032 26881084 53 ARID1A chr1 27022521 27108601 86081 PIGV chr1 27114453 27124894 10442 ZDHHC18 chr1 27153200 27182211 29012 SFN chr1 27189632 27190947 1316 GPN2 chr1 27205872 27216869 10998 GPATCH3 chr1 27216978 27226962 9985 NR0B2 chr1 27237974 27240567 2594 NUDC chr1 27248212 27273362 25151 C1orf172 chr1 27276046 27286901 10856 TRNP1 chr1 27320194 27327377 7184 FAM46B chr1 27331510 27339333 7824 SLC9A1 chr1 27425299 27481621 56323 WDTC1 chr1 27561006 27635110 74105 LOC644961 chr1 27650364 27653016 2653 TMEM222 chr1 27648635 27662891 14257 SYTL1 chr1 27668482 27680423 11942 MAP3K6 chr1 27681669 27693337 11669 FCN3 chr1 27695600 27701315 5716 CD164L2 chr1 27705595 27709805 4211 GPR3 chr1 27719151 27722317 3167 WASF2 chr1 27730733 27816678 85946 AHDC1 chr1 27860755 27930143 69389 FGR chr1 27938800 27961727 22928 IFI6 chr1 27992571 27998724 6154 FAM76A chr1 28052489 28089423 36935 STX12 chr1 28099693 28150963 51271 SCARNA1 chr1 28160911 28161077 167 PPP1R8 chr1 28157251 28178183 20933 THEMIS2 chr1 28199054 28213193 14140 RPA2 chr1 28218048 28241236 23189 SMPDL3B chr1 28261503 28285663 24161 XKR8 chr1 28286503 28294604 8102 EYA3 chr1 28296854 28415148 118295 PTAFR chr1 28473676 28520447 46772 DNAJC8 chr1 28526789 28559542 32754 ATPIF1 chr1 28562601 28564616 2016 SESN2 chr1 28585962 28609002 23041 MED18 chr1 28655512 28662478 6967 PHACTR4 chr1 28696092 28826881 130790 SNHG3 chr1 28832454 28837404 4951 RCC1 chr1 28832454 28865708 33255 TRNAU1AP chr1 28879528 28905057 25530 NUP210 chr3 13357736 13461809 104074 HDAC11 chr3 13521714 13547924 26211 FBLN2 chr3 13590624 13679922 89299 LINC00620 chr3 13692220 13788132 95913 WNT7A chr3 13860081 13921618 61538 LOC100132526 chr3 13974552 13978444 3893 TPRXL chr3 13978806 14107481 128676 CHCHD4 chr3 14153576 14166371 12796 TMEM43 chr3 14166439 14185180 18742 XPC chr3 14186647 14220172 33526 LSM3 chr3 14220227 14239869 19643 SLC6A6 chr3 14444105 14530857 86753 GRIP2 chr3 14530618 14583588 52971 CCDC174 chr3 14693252 14714166 20915 C3orf20 chr3 14716605 14814543 97939 FGD5 chr3 14860468 14976072 115605 FGD5-AS1 chr3 14984285 14989948 5664 NR2C2 chr3 14989235 15090780 101546 MRPS25 chr3 15090018 15106816 16799 ZFYVE20 chr3 15111579 15140655 29077 COL6A4P1 chr3 15206868 15247466 40599 CAPN7 chr3 15247732 15294423 46692 LOC100505696 chr3 15295690 15306005 10316 SH3BP5 chr3 15295862 15382901 87040 METTL6 chr3 15451376 15469042 17667 EAF1 chr3 15469063 15484120 15058 COLQ chr3 15491639 15563258 71620 MIR4270 chr3 15537745 15537815 71 HACL1 chr3 15602239 15643130 40892 BTD chr3 15643254 15687325 44072 ANKRD28 chr3 15708743 15901053 192311 MIR563 chr3 15915277 15915356 80 GALNTL2 chr3 16216183 16271253 55071 DPH3 chr3 16298567 16306496 7930 OXNAD1 chr3 16306666 16347594 40929 RFTN1 chr3 16357351 16555222 197872 DAZL chr3 16628300 16647006 18707 MIR3714 chr3 16974687 16974752 66 PLCL2 chr3 16926451 17132098 205648 TBC1D5 chr3 17198653 17784240 585588 LOC339862 chr3 18004063 18310410 306348 SATB1 chr3 18389132 18480265 91134 MIR4791 chr3 19356339 19356423 85 KCNH8 chr3 19190016 19577135 387120 EFHB chr3 19920965 19975706 54742 RAB5A chr3 19988571 20026667 38097 PP2D1 chr3 20021452 20053765 32314 KAT2B chr3 20081523 20195896 114374 SGOL1 chr3 20202084 20227724 25641 SGOL1-AS1 chr3 20215735 20227919 12185 VENTXP7 chr3 21447217 21448177 961 ZNF385D chr3 21462489 21792816 330328 UBE2E2 chr3 23244783 23632296 387514 MIR548AC chr3 23375625 23648882 273258 UBE2E1 chr3 23847383 23933131 85749 NKIRAS1 chr3 23933571 23958537 24967 RPL15 chr3 23958294 23965187 6894 NR1D2 chr3 23986750 24022109 35360 LOC152024 chr3 24141464 24144738 3275 THRB chr3 24158644 24536313 377670 LOC644990 chr3 24535577 24541502 5926 MIR4792 chr3 24562852 24562926 75 RARB chr3 25469753 25639422 169670 TOP2B chr3 25639474 25705788 66315 MIR4442 chr3 25706363 25706430 68 NGLY1 chr3 25760434 25831530 71097 OXSM chr3 25831562 25836025 4464 LOC285326 chr3 25900022 25915186 15165 LRRC3B chr3 26664299 26752265 87967 NEK10 chr3 27257096 27410912 153817 SLC4A7 chr3 27414211 27525911 111701 EOMES chr3 27757885 27763785 5901 CMC1 chr3 28283123 28361263 78141 AZI2 chr3 28363844 28390618 26775 ZCWPW2 chr3 28431986 28566632 134647 LOC645206 chr3 28616768 28799828 183061 RBMS3 chr3 29322802 30051886 729085 TGFBR2 chr3 30647993 30735633 87641 GADL1 chr3 30767691 30936153 168463 STT3B chr3 31574490 31677556 103067 OSBPL10-AS1 chr3 31745704 31763078 17375 OSBPL10 chr3 31702316 32023342 321027 ZNF860 chr3 32023265 32033228 9964 GPD1L chr3 32148002 32210207 62206 CMTM8 chr3 32280170 32411813 131644 CMTM7 chr3 32433162 32496333 63172 CMTM6 chr3 32522803 32544403 21601 DYNC1LI1 chr3 32567462 32612366 44905 DUSP22 chr6 292100 351355 59256 IRF4 chr6 391738 411443 19706 EXOC2 chr6 485137 693141 208005 HUS1B chr6 655938 656964 1027 LOC285768 chr6 961240 1101567 140328 FOXQ1 chr6 1312674 1314993 2320 FOXF2 chr6 1390068 1395832 5765 FOXC1 chr6 1610680 1614129 3450 GMDS chr6 1624034 2245868 621835 LOC100508120 chr6 2245986 2413825 167840 C6orf195 chr6 2622971 2635298 12328 MYLK4 chr6 2663862 2751154 87293 WRNIP1 chr6 2765665 2785979 20315 SERPINB1 chr6 2832565 2842283 9719 MIR4645 chr6 2854264 2854341 78 MGC39372 chr6 2854890 2876744 21855 SERPINB9 chr6 2887499 2903546 16048 SERPINB6 chr6 2948392 2972399 24008 DKFZP686I15217 chr6 2988200 2991405 3206 NQO2 chr6 3000066 3019994 19929 HTATSF1P2 chr6 3020389 3025005 4617 RIPK1 chr6 3077057 3115421 38365 BPHL chr6 3118925 3153432 34508 TUBB2A chr6 3153901 3157783 3883 LOC100507194 chr6 3183051 3196001 12951 TUBB2B chr6 3224494 3227968 3475 PSMG4 chr6 3259161 3268300 9140 SLC22A23 chr6 3269206 3456793 187588 PXDC1 chr6 3722835 3752246 29412 FAM50B chr6 3849631 3851551 1921 PRPF4B chr6 4021568 4065217 43650 FAM217A chr6 4068592 4079457 10866 C6orf201 chr6 4079439 4130999 51561 ECI2 chr6 4115926 4135831 19906 CDYL chr6 4706392 4955778 249387 RPP40 chr6 4995279 5004271 8993 PPP1R3G chr6 5085719 5087455 1737 MIR3691 chr6 5148466 5148556 91 LYRM4 chr6 5108652 5261172 152521 FARS2 chr6 5261583 5771816 510234 NRN1 chr6 5998232 6007633 9402 F13A1 chr6 6144310 6320924 176615 LY86-AS1 chr6 6346697 6623059 276363 LY86 chr6 6588933 6655216 66284 RREB1 chr6 7107829 7252213 144385 SSR1 chr6 7281287 7313541 32255 CAGE1 chr6 7326886 7389942 63057 RIOK1 chr6 7390061 7418270 28210 DSP chr6 7541869 7586946 45078 SNRNP48 chr6 7590431 7612200 21770 BMP6 chr6 7727010 7881961 154952 TXNDC5 chr6 7881482 7911047 29566 BLOC1S5-TXNDC5 chr6 7881482 8064647 183166 PIP5K1P1 chr6 7986334 7990577 4244 BLOC1S5 chr6 8013799 8064647 50849 EEF1E1-MUTED chr6 8013799 8102828 89030 SCARNA27 chr6 8086640 8086766 127 EEF1E1 chr6 8073592 8102828 29237 SLC35B3 chr6 8413300 8435794 22495 LOC100506207 chr6 8435855 8785678 349824 HULC chr6 8652441 8654080 1640 TFAP2A chr6 10396915 10419797 22883 LOC100130275 chr6 10412550 10416402 3853 LINC00518 chr6 10428017 10435055 7039 MIR5689 chr6 10439949 10440027 79 GCNT2 chr6 10521567 10629601 108035 C6orf52 chr6 10671650 10695030 23381 PAK1IP1 chr6 10695187 10709970 14784 TMEM14C chr6 10723147 10731362 8216 TMEM14B chr6 10747994 10757214 9221 MAK chr6 10762955 10838788 75834 GCM2 chr6 10873455 10882098 8644 SYCP2L chr6 10887063 10974541 87479 ELOVL2 chr6 10980992 11044624 63633 ELOVL2-AS1 chr6 11043990 11079377 35388 ERVFRD-1 chr6 11102721 11112071 9351 C6orf228 chr6 11094265 11138969 44705 NEDD9 chr6 11183530 11382581 199052 TMEM170B chr6 11538510 11583757 45248 ADTRP chr6 11713887 11779280 65394 HIVEP1 chr6 12012723 12165232 152510 EDN1 chr6 12290528 12297427 6900 RNU6-48 chr6 12392558 12392586 29 PHACTR1 chr6 12717036 13288075 571040 LOC100130357 chr6 13279526 13295818 16293 TBC1D7 chr6 13305183 13328787 23605 GFOD1 chr6 13363586 13487869 124284 SIRT5 chr6 13574760 13615390 40631 NOL7 chr6 13615558 13621127 5570 RANBP9 chr6 13621729 13711796 90068 CCDC90A chr6 13786780 13814792 28013 RNF182 chr6 13924676 13980240 55565 CD83 chr6 14117486 14137148 19663 JARID2 chr6 15246205 15522273 276069 DTNBP1 chr6 15523031 15663289 140259
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    bioRxiv preprint doi: https://doi.org/10.1101/869560; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Beyond accessibility: ATAC-seq footprinting unravels kinetics 2 of transcription factor binding during zygotic genome 3 activation 4 Authors 5 Mette Bentsen1, Philipp Goymann1, Hendrik Schultheis1, Kathrin Klee1, Anastasiia Petrova1, 6 René Wiegandt1, Annika Fust1, Jens Preussner1,3, Carsten Kuenne1, Thomas Braun2,3, 7 Johnny Kim2,3, Mario Looso1,3 8 Affiliation 9 1 Bioinformatics Core Unit (BCU), Max Planck Institute for Heart and Lung Research, Bad 10 Nauheim, Germany 11 2 Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and 12 Lung Research, Bad Nauheim, Germany 13 3 German Centre for Cardiovascular Research (DZHK), Partner site Rhein-Main, Frankfurt am 14 Main, 60596 Germany 15 Corresponding author email address 16 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/869560; this version posted February 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 17 Abstract 18 While footprinting analysis of ATAC-seq data can theoretically enable investigation of 19 transcription factor (TF) binding, the lack of a computational tool able to conduct different 20 levels of footprinting analysis has so-far hindered the widespread application of this method. 21 Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework 22 enabling genome-wide investigation of TF binding dynamics for hundreds of TFs 23 simultaneously.
  • The Tumor Suppressor Notch Inhibits Head and Neck Squamous Cell

    The Tumor Suppressor Notch Inhibits Head and Neck Squamous Cell

    The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 12-2015 THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN) Shhyam Moorthy Shhyam Moorthy Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Biochemistry, Biophysics, and Structural Biology Commons, Cancer Biology Commons, Cell Biology Commons, and the Medicine and Health Sciences Commons Recommended Citation Moorthy, Shhyam and Moorthy, Shhyam, "THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN)" (2015). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 638. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/638 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. THE TUMOR SUPPRESSOR NOTCH INHIBITS HEAD AND NECK SQUAMOUS CELL CARCINOMA (HNSCC) TUMOR GROWTH AND PROGRESSION BY MODULATING PROTO-ONCOGENES AXL AND CTNNAL1 (α-CATULIN) by Shhyam Moorthy, B.S.
  • An Evolutionary Based Strategy for Predicting Rational Mutations in G Protein-Coupled Receptors

    An Evolutionary Based Strategy for Predicting Rational Mutations in G Protein-Coupled Receptors

    Ecology and Evolutionary Biology 2021; 6(3): 53-77 http://www.sciencepublishinggroup.com/j/eeb doi: 10.11648/j.eeb.20210603.11 ISSN: 2575-3789 (Print); ISSN: 2575-3762 (Online) An Evolutionary Based Strategy for Predicting Rational Mutations in G Protein-Coupled Receptors Miguel Angel Fuertes*, Carlos Alonso Department of Microbiology, Centre for Molecular Biology “Severo Ochoa”, Spanish National Research Council and Autonomous University, Madrid, Spain Email address: *Corresponding author To cite this article: Miguel Angel Fuertes, Carlos Alonso. An Evolutionary Based Strategy for Predicting Rational Mutations in G Protein-Coupled Receptors. Ecology and Evolutionary Biology. Vol. 6, No. 3, 2021, pp. 53-77. doi: 10.11648/j.eeb.20210603.11 Received: April 24, 2021; Accepted: May 11, 2021; Published: July 13, 2021 Abstract: Capturing conserved patterns in genes and proteins is important for inferring phenotype prediction and evolutionary analysis. The study is focused on the conserved patterns of the G protein-coupled receptors, an important superfamily of receptors. Olfactory receptors represent more than 2% of our genome and constitute the largest family of G protein-coupled receptors, a key class of drug targets. As no crystallographic structures are available, mechanistic studies rely on the use of molecular dynamic modelling combined with site-directed mutagenesis data. In this paper, we hypothesized that human-mouse orthologs coding for G protein-coupled receptors maintain, at speciation events, shared compositional structures independent, to some extent, of their percent identity as reveals a method based in the categorization of nucleotide triplets by their gross composition. The data support the consistency of the hypothesis, showing in ortholog G protein-coupled receptors the presence of emergent shared compositional structures preserved at speciation events.
  • Antibody List

    Antibody List

    產品編號 產品名稱 PA569955 1110059E24Rik Polyclonal Antibody PA569956 1110059E24Rik Polyclonal Antibody PA570131 1190002N15Rik Polyclonal Antibody 01-1234-42 123count eBeads Counting Beads MA512242 14.3.3 Pan Monoclonal Antibody (CG15) LFMA0074 14-3-3 beta Monoclonal Antibody (60C10) LFPA0077 14-3-3 beta Polyclonal Antibody PA137002 14-3-3 beta Polyclonal Antibody PA14647 14-3-3 beta Polyclonal Antibody PA515477 14-3-3 beta Polyclonal Antibody PA517425 14-3-3 beta Polyclonal Antibody PA522264 14-3-3 beta Polyclonal Antibody PA529689 14-3-3 beta Polyclonal Antibody MA134561 14-3-3 beta/epsilon/zeta Monoclonal Antibody (3C8) MA125492 14-3-3 beta/zeta Monoclonal Antibody (22-IID8B) MA125665 14-3-3 beta/zeta Monoclonal Antibody (4E2) 702477 14-3-3 delta/zeta Antibody (1H9L19), ABfinity Rabbit Monoclonal 711507 14-3-3 delta/zeta Antibody (1HCLC), ABfinity Rabbit Oligoclonal 702241 14-3-3 epsilon Antibody (5H10L5), ABfinity Rabbit Monoclonal 711273 14-3-3 epsilon Antibody (5HCLC), ABfinity Rabbit Oligoclonal PA517104 14-3-3 epsilon Polyclonal Antibody PA528937 14-3-3 epsilon Polyclonal Antibody PA529773 14-3-3 epsilon Polyclonal Antibody PA575298 14-3-3 eta (Lys81) Polyclonal Antibody MA524792 14-3-3 eta Monoclonal Antibody PA528113 14-3-3 eta Polyclonal Antibody PA529774 14-3-3 eta Polyclonal Antibody PA546811 14-3-3 eta Polyclonal Antibody MA116588 14-3-3 gamma Monoclonal Antibody (HS23) MA116587 14-3-3 gamma Monoclonal Antibody (KC21) PA529690 14-3-3 gamma Polyclonal Antibody PA578233 14-3-3 gamma Polyclonal Antibody 510700 14-3-3 Pan Polyclonal