DOCSLIB.ORG

Supplementary Table 1: Tandem Minigene Constructs for Patient 3784

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Table 1: Tandem Minigene Constructs for Patient 3784 Supplementary Table 1: Tandem minigene constructs for patient 3784 TMG Gene aa position wt aa mut aa wild type amino acid sequence mutated amino acid sequence mutation type TMG1 ABHD16A 322 P S WNHPGFAGSTGVPFPQNEANAMDVV WNHPGFAGSTGVSFPQNEANAMDVV Substitution ALMS1 892 P F HLTEEALKVSIVPGPGDQKTGIPSA HLTEEALKVSIVFGPGDQKTGIPSA Substitution ANKHD1-EIF4EBP3 1555 P S RKNKKNKTKETPPTAHLILPEQHMS RKNKKNKTKETPSTAHLILPEQHMS Substitution ATP8B1 946 R K RLLLVHGRWSYIRMCKFLRYFFYKN RLLLVHGRWSYIKMCKFLRYFFYKN Substitution ATR 1405 L F AYGLLMELTRAYLAYADNSRAQDSA AYGLLMELTRAYFAYADNSRAQDSA Substitution ATXN7 780 P L VNVRHDQSGRGPPTGSPAESIKRMS VNVRHDQSGRGPLTGSPAESIKRMS Substitution B4GALT5 326 S F VSRPEGDTGKYKSIPHHHRGEVQFL VSRPEGDTGKYKFIPHHHRGEVQFL Substitution BLM 1351 A V MPASQRSKRRKTASSGSKAKGGSAT MPASQRSKRRKTVSSGSKAKGGSAT Substitution BRAF 600 V E LTVKIGDFGLATVKSRWSGSHQFEQ LTVKIGDFGLATEKSRWSGSHQFEQ Substitution BRAT1 418 T I APASSVGGHLCGTLAGCVRVQRAAL APASSVGGHLCGILAGCVRVQRAAL Substitution BRD9 554 S F GGSRPSSNLSSLSNASERDQHHLGS GGSRPSSNLSSLFNASERDQHHLGS Substitution BRF1 109 T I GNQLQLNQHCLDTAFNFFKMAVSRH GNQLQLNQHCLDIAFNFFKMAVSRH Substitution C11orf30 992 P L IHLQADQLQHKLPQMPQLSIRHQKL IHLQADQLQHKLLQMPQLSIRHQKL Substitution C2CD3 486 S L SKKISQSTALARSSKVLESSDHKLK SKKISQSTALARLSKVLESSDHKLK Substitution CAMKK2 124 P L GGSLDMNGRCICPSLPYSPVSSPQS GGSLDMNGRCICLSLPYSPVSSPQS Substitution CD164 50 L P PISNVTSAPVTSLPLVTTPAPETCE PISNVTSAPVTSPPLVTTPAPETCE Substitution TMG2 CDCA3 145 P S EEQMPPWNQTEFPSKQVFSKEEARQ EEQMPPWNQTEFSSKQVFSKEEARQ Substitution CDK13 757 R W FPITAIREIKILRQLTHQSIINMKE FPITAIREIKILWQLTHQSIINMKE Substitution CHPF 629 R C DTVLTPDFLNRCRMHAISGWQAFFP DTVLTPDFLNRCCMHAISGWQAFFP Substitution CLEC4F 19 P S RFCTDNQCVSLHPQEVDSVAMAPAA RFCTDNQCVSLHSQEVDSVAMAPAA Substitution COL5A2 1110 G E GQRGDPGSRGPIGPPGRAGKRGLPG GQRGDPGSRGPIEPPGRAGKRGLPG Substitution COL7A1 1412 G E GDKGDRGERGPPGPGEGGIAPGEPG GDKGDRGERGPPEPGEGGIAPGEPG Substitution CTSC 42 CTYLDLLGTWVFQVG … CTYLDLLGTWVFRWAPAVPSAMSTARLWDHKKKK Frameshift CTTN 261 S F GWDHQEKLQLHESQKDYKTGFGGKF GWDHQEKLQLHEFQKDYKTGFGGKF Substitution CTTN 261 S F GWDHQEKLQLHESQKDYSKGFGGKY GWDHQEKLQLHEFQKDYSKGFGGKY Substitution DBF4 16 P L KELVVVHKKQEKPCSPFDVDKPSSM KELVVVHKKQEKLCSPFDVDKPSSM Substitution DBF4 249 P L TNMPFINYSIQKPCSPFDVDKPSSM TNMPFINYSIQKLCSPFDVDKPSSM Substitution DCLRE1A 1009 P H YLEMKRFVQWLKPQKIIPTVNVGTW YLEMKRFVQWLKHQKIIPTVNVGTW Substitution DDX42 565 P L VATDVAARGLDIPSIKTVINYDVAR VATDVAARGLDILSIKTVINYDVAR Substitution DHX16 573 P S STFFDDAPVFRIPGRRFPVDIFYTK STFFDDAPVFRISGRRFPVDIFYTK Substitution DOLPP1 111 S F MPSSHSQFMWFFSVYSFLFLYLRMH MPSSHSQFMWFFFVYSFLFLYLRMH Substitution DTNA 87 T I ELNVSRLEAVLSTIFYQLNKRMPTT ELNVSRLEAVLSIIFYQLNKRMPTT Substitution TMG3 DTNB 110 L F STHQISVEQSISLLLNFMIAAYDSE STHQISVEQSISFLLNFMIAAYDSE Substitution ENSG00000006634 229 P S KPFVKVEDMSQSPAVHLM KPFVKVEDMSQSSAVHLM Substitution ENSG00000089902 35 T M SGNMAEIFRQSQT SGNMAEIFRQSQM Substitution ENSG00000099995 32 S F KQPLVRRSVRRRSRSQRKR KQPLVRRSVRRRFRSQRKR Substitution ENSG00000163738 3 P L MDPRVSGILVQLPLPDHVDERTICN MDLRVSGILVQLPLP Substitution ENSG00000164124 160 P L EIPNNTCSMDTTPLITEHGLQSCSD EIPNNTCSMDTTLLITEHGLQSCSD Substitution ENSG00000164124 160 P L EIPNNTCSMDTTPLITEHVSIV EIPNNTCSMDTTLLITEHVSIV Substitution ENSG00000187098 103 P L KFEEQNRAESECPDG KFEEQNRAESECLDG Substitution EPHA2 643 V M MLKTSSGKKEVPVAIKTLKAGYTEK MLKTSSGKKEVPMAIKTLKAGYTEK Substitution ESPL1 1380 A V VCPTESKPEVPQAPRVQQRVQTRLK VCPTESKPEVPQVPRVQQRVQTRLK Substitution EXOC3 49 A V ARKKASVEARLKAAIQSQLDGVRTG ARKKASVEARLKVAIQSQLDGVRTG Substitution EXOC4 423 R Q EPSAQLSYASTGREFAAFFAKKKPQ EPSAQLSYASTGQEFAAFFAKKKPQ Substitution FKTN 359 G E GKVEDSLELSFQGKDDVKLDVFFFY GKVEDSLELSFQEKDDVKLDVFFFY Substitution FLNA 2049 R C VVISQSEIGDASRVRVSGQGLHEGH VVISQSEIGDASCVRVSGQGLHEGH Substitution FLNC 2595 P S IVGSPFKAKVTGPRLSGGHSLHETS IVGSPFKAKVTGSRLSGGHSLHETS Substitution FREM1 1200 G E TQKPRHGLLIDRGFSKDFSENKQPA TQKPRHGLLIDREFSKDFSENKQPA Substitution TMG4 FSCN1 484 T A GDHAGVLKASAETVDPASLWEY GDHAGVLKASAEAVDPASLWEY Substitution GAA 144 S F SYPSYKLENLSSSEMGYTATLTRTT SYPSYKLENLSSFEMGYTATLTRTT Substitution GNB5 84 P S DMKTALALYEFPPMGLLSALDHGII DMKTALALYEFPSMGLLSALDHGII Substitution GNB5 377 P L GHENRVSTLRVSPDGTAFCSGSWDH GHENRVSTLRVSLDGTAFCSGSWDH Substitution GPATCH8 865 S F RSRSGRRHSSHRSSRRSYSSSSDAS RSRSGRRHSSHRFSRRSYSSSSDAS Substitution GPR98 6009 R Q YVLVMNDEHTERRYLLFFLLSWGLP YVLVMNDEHTERQYLLFFLLSWGLP Substitution GPRIN1 887 P L PMTPQAAAPPAFPEVRVRPGSALAA PMTPQAAAPPAFLEVRVRPGSALAA Substitution GSE1 718 R Q LKPGSPYRPPVPRAPDPAYIYDEFL LKPGSPYRPPVPQAPDPAYIYDEFL Substitution HIF3A 17 E K LQRARSTTELRKEKSRDAARSRRSQ LQRARSTTELRKKKSRDAARSRRSQ Substitution HIF3A 15 E K WQDHRSTTELRKEKSRDAARSRRSQ WQDHRSTTELRKKKSRDAARSRRSQ Substitution IFIT5 98 G E SDKEEVRSLVTWGNYAWVYYHMDQL SDKEEVRSLVTWENYAWVYYHMDQL Substitution IFT140 1141 R K CSDFFIEHSQYERAVELLLAARKYQ CSDFFIEHSQYEKAVELLLAARKYQ Substitution IK 555 P L KKMEADGVEVKRPKY KKMEADGVEVKRLKY Substitution INF2 196 T I ELSGSDNVPYVVTLLSVINAVILGP ELSGSDNVPYVVILLSVINAVILGP Substitution IRF2BP1 7 S F MASVQASRRQWCYLCDLPKMPWAMV MASVQAFRRQWCYLCDLPK Substitution ITCH 831 V I IDNEKRMRLLQFVTGTCRLPVGGFA IDNEKRMRLLQFITGTCRLPVGGFA Substitution TMG5 ITPR3 290 H N SSNALWEVEVVHHDPCRGGAGHWNG SSNALWEVEVVHNDPCRGGAGHWNG Substitution KAZN 409 T I QRKSLDPGLFDGTAPDYYIEEDADW QRKSLDPGLFDGIAPDYYIEEDADW Substitution KDM7A 758 D N YSTCLQRQIQSTDCSGERNSLQDPS YSTCLQRQIQSTNCSGERNSLQDPS Substitution KIF16B 1009 L P REKQQREALERALARLERRHSALQR REKQQREALERAPARLERRHSALQR Substitution KRT10 547 S Y SGGGGGGYGGGSSGGGSSSGGGYGG SGGGGGGYGGGSYGGGSSSGGGYGG Substitution LPHN2 803 R Q TQGCKLVDTNKTRTTCACSHLTNFA TQGCKLVDTNKTQTTCACSHLTNFA Substitution LTBP4 281 P L DDFEALCNVLRPPAYSPPRPGGFGL DDFEALCNVLRPLAYSPPRPGGFGL Substitution MBNL2 119 G S GTPLHPVPTFPVGPAIGTNTAISFA GTPLHPVPTFPVSPAIGTNTAISFA Substitution MED4 173 R W VCAPLTWVPGDPRRPYPTDLEMRSG VCAPLTWVPGDPWRPYPTDLEMRSG Substitution MFI2 190 R K ETSYSESLCRLCRGDSSGEGVCDKS ETSYSESLCRLCKGDSSGEGVCDKS Substitution MITF 194 P L KFEEQNRAESECPGMNTHSRASCMQ KFEEQNRAESECLGMNTHSRASCMQ Substitution MOSPD3 141 P L KDITSILRAPAYPLELQGQPDPAPR KDITSILRAPAYLLELQGQPDPAPR Substitution MTHFD2L 138 P L ELLDVTDQLNMDPRVSGILVQLPLP ELLDVTDQLNMDLRVSGILVQLPLP Substitution MYH9 1576 R Q AMKAQFERDLQGRDEQSEEKKKQLV AMKAQFERDLQGQDEQSEEKKKQLV Substitution NBPF9 217 M I VSAGPLSSEKAEMNILEINEKLHPQ VSAGPLSSEKAEINILEINEKLHPQ Substitution NCLN 202 A V GVQSKAVSDWLIASVEGRLTGLGGE GVQSKAVSDWLIVSVEGRLTGLGGE Substitution TMG6 NCOA2 593 S F DSKDCFGLYGEPSEGTTGQAESSCH DSKDCFGLYGEPFEGTTGQAESSCH Substitution NELL1 433 E K GYISVQGDSAYCEDIDECAAKMHYC GYISVQGDSAYCKDIDECAAKMHYC Substitution NFKB1 618 S F GADLSLLDRLGNSVLHLAAKEGHDK GADLSLLDRLGNFVLHLAAKEGHDK Substitution NOL6 380 Q L TMSGYQVLRSVLQFLATTDLTVNGI TMSGYQVLRSVLLFLATTDLTVNGI Substitution NOL6 380 Q L TMSGYQVLRSVLQFLDLTVNGISLC TMSGYQVLRSVLLFLDLTVNGISLC Substitution NOL8 291 R C KLHSLIGLGIKNRVSCHDSDDDIMR KLHSLIGLGIKNCVSCHDSDDDIMR Substitution NPIPB5 388 P L PLPPSADDNLKTPSERQLTPLPPSA PLPPSADDNLKTLSERQLTPLPPSA Substitution NQO2 103 P S KVREADLVIFQFPLYWFSVPAILKG KVREADLVIFQFSLYWFSVPAILKG Substitution PABPC5 183 P L NNRQVYVGRFKFPEERAAEVRTRDR NNRQVYVGRFKFLEERAAEVRTRDR Substitution PAM 861 G D KMQEKQKLIKEPGSGVPVVLITTLL KMQEKQKLIKEPDSGVPVVLITTLL Substitution PARP10 1015 P L TCEHVPRASPDDPSGLPGRSPDT TCEHVPRASPDDLSGLPGRSPDT Substitution PCDH18 886 D N GRGDSEAGDSDYDLGRDSPIDRLLG GRGDSEAGDSDYNLGRDSPIDRLLG Substitution PCSK7 14 P L PKGRQKVPHLDAPLGLPTCLWLELA PKGRQKVPHLDALLGLPTCLWLELA Substitution PHIP 166 P L KLNGKYRLERLVPTAVYQHMKMHKR KLNGKYRLERLVLTAVYQHMKMHKR Substitution PHOSPHO2-KLHL23 268 S F IYNALNPMHKEISQRSTATMYIIGG IYNALNPMHKEIFQRSTATMYIIGG Substitution PI4K2A 162 L F VFKPKNEEPYGHLNPKWTKWLQKLC VFKPKNEEPYGHFNPKWTKWLQKLC Substitution TMG7 PRR14L 2020 P S KKVSQIRIRKTIPRPDPNLTPMGLP KKVSQIRIRKTISRPDPNLTPMGLP Substitution PRRC2A 1098 P S ETRSEGSEYEEIPKRRRQRGSETGS ETRSEGSEYEEISKRRRQRGSETGS Substitution PTPN11 426 H Y TVWQYHFRTWPDHGVPSDPGGVLDF TVWQYHFRTWPDYGVPSDPGGVLDF Substitution RALGDS 629 H Y AALQPAGGRLLYHPRQPGRGQWQHV AALQPAGGRLLYYPRQPGRGQWQHV Substitution RAP1GDS1 571 E K ICALMGSECLHKEVQDLAFLDVVSK ICALMGSECLHKKVQDLAFLDVVSK Substitution RNF145 256 P S ALGMSLWNQLVVPVLFMVFWLVLFA ALGMSLWNQLVVSVLFMVFWLVLFA Substitution RPL11 97 NFS NS GLKVREYELRKNNFSDTGNFGFGIQ GLKVREYELRKNNSDTGNFGFGIQE deletion RRBP1 436 Q P GAQNQGKKAEGAQNQGKKAEGAQNQ GAQNQGKKAEGAPNQGKKAEGAQNQ Substitution SCRIB 1561 S F TPVEDLGPQTSTSPGRLPLSGKKFD TPVEDLGPQTSTFPGRLPLSGKKFD Substitution SCRIB 1561 S F TPVEDLGPQTSTSPGRLSPDFAEEL TPVEDLGPQTSTFPGRLSPDFAEEL Substitution SEC31A 435 E K QQHHVFISQVVTEKEFLSRSDQLQQ QQHHVFISQVVTKKEFLSRSDQLQQ Substitution SENP5 503 L F ASPVDDEQLSVCLSGFLDEVMKKYG ASPVDDEQLSVCFSGFLDEVMKKYG Substitution SERINC2 143 L F GLVLLRRRGLLPLHPHPAGAAHRLC GLVLLRRRGLLPFHPHPAGAAHRLC Substitution SETD2 1501 C Y KSHRDIKRMQCECTPLSKDERAQGE KSHRDIKRMQCEYTPLSKDERAQGE Substitution SH3TC2 243 H Y LVSALEPLPLPFHQWFLKNYPGSCG LVSALEPLPLPFYQWFLKNYPGSCG Substitution SLC30A5 594 L P GGGMNANMRGVFLHVLADTLGSIGV GGGMNANMRGVFPHVLADTLGSIGV Substitution TMG8 SLIT2 715 G E QDVAIQDFTCDDGNDDNSCSPLSRC QDVAIQDFTCDDENDDNSCSPLSRC Substitution SNW1 499 F L GREGPVQFEEDPFGLDKFLEEAKQH GREGPVQFEEDPLGLDKFLEEAKQH Substitution SON 1927 R C RKTVRARSRTPSRRSRSHTPSRRRR RKTVRARSRTPSCRSRSHTPSRRRR Substitution SPATA20 285 P S EEYGGFAEAPKFPTPVILSFLFSYW EEYGGFAEAPKFSTPVILSFLFSYW Substitution ST6GALNAC3 252 P L DTYCKTEGYRKVPYHYYEQGRDECD DTYCKTEGYRKVLYHYYEQGRDECD Substitution ST6GALNAC3 151 P L TGKDRTEGYRKVPYHYYEQGRDECD TGKDRTEGYRKVLYHYYEQGRDECD Substitution STS 532 E K EPRFYEILKVMQEAADRHTQTLPEV EPRFYEILKVMQKAADRHTQTLPEV Substitution SZT2 1576 S
Load more

Recommended publications
  • Gene PMID WBS Locus ABR 26603386 AASDH 26603386
    Supplementary material J Med Genet Gene PMID WBS Locus ABR 26603386 AASDH 26603386 ABCA1 21304579 ABCA13 26603386 ABCA3 25501393 ABCA7 25501393 ABCC1 25501393 ABCC3 25501393 ABCG1 25501393 ABHD10 21304579 ABHD11 25501393 yes ABHD2 25501393 ABHD5 21304579 ABLIM1 21304579;26603386 ACOT12 25501393 ACSF2,CHAD 26603386 ACSL4 21304579 ACSM3 26603386 ACTA2 25501393 ACTN1 26603386 ACTN3 26603386;25501393;25501393 ACTN4 21304579 ACTR1B 21304579 ACVR2A 21304579 ACY3 19897463 ACYP1 21304579 ADA 25501393 ADAM12 21304579 ADAM19 25501393 ADAM32 26603386 ADAMTS1 25501393 ADAMTS10 25501393 ADAMTS12 26603386 ADAMTS17 26603386 ADAMTS6 21304579 ADAMTS7 25501393 ADAMTSL1 21304579 ADAMTSL4 25501393 ADAMTSL5 25501393 ADCY3 25501393 ADK 21304579 ADRBK2 25501393 AEBP1 25501393 AES 25501393 AFAP1,LOC84740 26603386 AFAP1L2 26603386 AFG3L1 21304579 AGAP1 26603386 AGAP9 21304579 Codina-Sola M, et al. J Med Genet 2019; 56:801–808. doi: 10.1136/jmedgenet-2019-106080 Supplementary material J Med Genet AGBL5 21304579 AGPAT3 19897463;25501393 AGRN 25501393 AGXT2L2 25501393 AHCY 25501393 AHDC1 26603386 AHNAK 26603386 AHRR 26603386 AIDA 25501393 AIFM2 21304579 AIG1 21304579 AIP 21304579 AK5 21304579 AKAP1 25501393 AKAP6 21304579 AKNA 21304579 AKR1E2 26603386 AKR7A2 21304579 AKR7A3 26603386 AKR7L 26603386 AKT3 21304579 ALDH18A1 25501393;25501393 ALDH1A3 21304579 ALDH1B1 21304579 ALDH6A1 21304579 ALDOC 21304579 ALG10B 26603386 ALG13 21304579 ALKBH7 25501393 ALPK2 21304579 AMPH 21304579 ANG 21304579 ANGPTL2,RALGPS1 26603386 ANGPTL6 26603386 ANK2 21304579 ANKMY1 26603386 ANKMY2
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [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]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [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]
  • Investigation of Candidate Genes and Mechanisms Underlying Obesity
    Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between
    [Show full text]
  • Cellular and Molecular Signatures in the Disease Tissue of Early
    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
    [Show full text]
  • Gene Standard Deviation MTOR 0.12553731 PRPF38A
    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) Gut Gene Standard Deviation MTOR 0.12553731 PRPF38A 0.141472605 EIF2B4 0.154700091 DDX50 0.156333027 SMC3 0.161420017 NFAT5 0.166316903 MAP2K1 0.166585267 KDM1A 0.16904912 RPS6KB1 0.170330192 FCF1 0.170391706 MAP3K7 0.170660513 EIF4E2 0.171572093 TCEB1 0.175363093 CNOT10 0.178975095 SMAD1 0.179164705 NAA15 0.179904998 SETD2 0.180182498 HDAC3 0.183971158 AMMECR1L 0.184195031 CHD4 0.186678211 SF3A3 0.186697697 CNOT4 0.189434633 MTMR14 0.189734199 SMAD4 0.192451524 TLK2 0.192702667 DLG1 0.19336621 COG7 0.193422331 SP1 0.194364189 PPP3R1 0.196430217 ERBB2IP 0.201473001 RAF1 0.206887192 CUL1 0.207514271 VEZF1 0.207579584 SMAD3 0.208159809 TFDP1 0.208834504 VAV2 0.210269344 ADAM17 0.210687138 SMURF2 0.211437666 MRPS5 0.212428684 TMUB2 0.212560675 SRPK2 0.216217428 MAP2K4 0.216345366 VHL 0.219735582 SMURF1 0.221242495 PLCG1 0.221688351 EP300 0.221792349 Sundar R, et al. Gut 2020;0:1–10. doi: 10.1136/gutjnl-2020-320805 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) Gut MGAT5 0.222050228 CDC42 0.2230598 DICER1 0.225358787 RBX1 0.228272533 ZFYVE16 0.22831803 PTEN 0.228595789 PDCD10 0.228799406 NF2 0.23091035 TP53 0.232683696 RB1 0.232729172 TCF20 0.2346075 PPP2CB 0.235117302 AGK 0.235416298
    [Show full text]
  • Myopia in African Americans Is Significantly Linked to Chromosome 7P15.2-14.2
    Genetics Myopia in African Americans Is Significantly Linked to Chromosome 7p15.2-14.2 Claire L. Simpson,1,2,* Anthony M. Musolf,2,* Roberto Y. Cordero,1 Jennifer B. Cordero,1 Laura Portas,2 Federico Murgia,2 Deyana D. Lewis,2 Candace D. Middlebrooks,2 Elise B. Ciner,3 Joan E. Bailey-Wilson,1,† and Dwight Stambolian4,† 1Department of Genetics, Genomics and Informatics and Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, Tennessee, United States 2Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States 3The Pennsylvania College of Optometry at Salus University, Elkins Park, Pennsylvania, United States 4Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, United States Correspondence: Joan E. PURPOSE. The purpose of this study was to perform genetic linkage analysis and associ- Bailey-Wilson, NIH/NHGRI, 333 ation analysis on exome genotyping from highly aggregated African American families Cassell Drive, Suite 1200, Baltimore, with nonpathogenic myopia. African Americans are a particularly understudied popula- MD 21131, USA; tion with respect to myopia. [email protected]. METHODS. One hundred six African American families from the Philadelphia area with a CLS and AMM contributed equally to family history of myopia were genotyped using an Illumina ExomePlus array and merged this work and should be considered co-first authors. with previous microsatellite data. Myopia was initially measured in mean spherical equiv- JEB-W and DS contributed equally alent (MSE) and converted to a binary phenotype where individuals were identified as to this work and should be affected, unaffected, or unknown.
    [Show full text]
  • Identification of Transcriptomic Differences Between Lower
    International Journal of Molecular Sciences Article Identification of Transcriptomic Differences between Lower Extremities Arterial Disease, Abdominal Aortic Aneurysm and Chronic Venous Disease in Peripheral Blood Mononuclear Cells Specimens Daniel P. Zalewski 1,*,† , Karol P. Ruszel 2,†, Andrzej St˛epniewski 3, Dariusz Gałkowski 4, Jacek Bogucki 5 , Przemysław Kołodziej 6 , Jolanta Szyma ´nska 7 , Bartosz J. Płachno 8 , Tomasz Zubilewicz 9 , Marcin Feldo 9,‡ , Janusz Kocki 2,‡ and Anna Bogucka-Kocka 1,‡ 1 Chair and Department of Biology and Genetics, Medical University of Lublin, 4a Chod´zkiSt., 20-093 Lublin, Poland; [email protected] 2 Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, 11 Radziwiłłowska St., 20-080 Lublin, Poland; [email protected] (K.P.R.); [email protected] (J.K.) 3 Ecotech Complex Analytical and Programme Centre for Advanced Environmentally Friendly Technologies, University of Marie Curie-Skłodowska, 39 Gł˛ebokaSt., 20-612 Lublin, Poland; [email protected] 4 Department of Pathology and Laboratory Medicine, Rutgers-Robert Wood Johnson Medical School, One Robert Wood Johnson Place, New Brunswick, NJ 08903-0019, USA; [email protected] 5 Chair and Department of Organic Chemistry, Medical University of Lublin, 4a Chod´zkiSt., Citation: Zalewski, D.P.; Ruszel, K.P.; 20-093 Lublin, Poland; [email protected] St˛epniewski,A.; Gałkowski, D.; 6 Laboratory of Diagnostic Parasitology, Chair and Department of Biology and Genetics, Medical University of Bogucki, J.; Kołodziej, P.; Szyma´nska, Lublin, 4a Chod´zkiSt., 20-093 Lublin, Poland; [email protected] J.; Płachno, B.J.; Zubilewicz, T.; Feldo, 7 Department of Integrated Paediatric Dentistry, Chair of Integrated Dentistry, Medical University of Lublin, M.; et al.
    [Show full text]
  • Open Full Page
    Published OnlineFirst August 15, 2016; DOI: 10.1158/1078-0432.CCR-16-0290 Biology of Human Tumors Clinical Cancer Research Recurrent TRIO Fusion in Nontranslocation– Related Sarcomas Lucile Delespaul1,2, Tom Lesluyes1,2,Gaelle€ Perot 1,3,Celine Brulard1, Lydia Lartigue1,2, Jessica Baud1,2, Pauline Lagarde1, Sophie Le Guellec4,Agnes Neuville1,3, Philippe Terrier5, Dominique Vince-Ranchere 6, Susanne Schmidt7, Anne Debant7, Jean-Michel Coindre1,2,3, and Fred eric Chibon1,3 Abstract Purpose: Despite various differences, nontranslocation-related with various partners, was identified in 5.1% of cases. TRIO sarcomas (e.g., comprising undifferentiated pleomorphic sarcoma, translocations are either intrachromosomal with TERT or inter- leiomyosarcoma, myxofibrosarcoma) are unified by their complex chromosomal with LINC01504 or ZNF558. Our results suggest genetics. Extensive analysis of the tumor genome using molecular that all translocations led to a truncated TRIO protein either cytogenetic approaches showed many chromosomal gains, losses, directly or indirectly by alternative splicing. TRIO rearrangement and translocations per cell. Genomic quantitative alterations and is associated with a modified transcriptomic program to immu- expression variations have been extensively studied by adapted nity/inflammation, proliferation and migration, and an increase high-throughput approaches, yet translocations still remained in proliferation. unscreened. We therefore analyzed 117 nontranslocation-related Conclusions: TRIO fusions have been identified in four
    [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]