DOCSLIB.ORG

Supplemental Table 3 Two-Class Paired Significance Analysis of Microarrays Comparing Gene Expression Between Paired

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplemental Table 3 Two-Class Paired Significance Analysis of Microarrays Comparing Gene Expression Between Paired Supplemental Table 3 Two‐class paired Significance Analysis of Microarrays comparing gene expression between paired pre‐ and post‐transplant kidneys biopsies (N=8). Entrez Fold q‐value Probe Set ID Gene Symbol Unigene Name Score Gene ID Difference (%) Probe sets higher expressed in post‐transplant biopsies in paired analysis (N=1871) 218870_at 55843 ARHGAP15 Rho GTPase activating protein 15 7,01 3,99 0,00 205304_s_at 3764 KCNJ8 potassium inwardly‐rectifying channel, subfamily J, member 8 6,30 4,50 0,00 1563649_at ‐‐ ‐‐ ‐‐ 6,24 3,51 0,00 1567913_at 541466 CT45‐1 cancer/testis antigen CT45‐1 5,90 4,21 0,00 203932_at 3109 HLA‐DMB major histocompatibility complex, class II, DM beta 5,83 3,20 0,00 204606_at 6366 CCL21 chemokine (C‐C motif) ligand 21 5,82 10,42 0,00 205898_at 1524 CX3CR1 chemokine (C‐X3‐C motif) receptor 1 5,74 8,50 0,00 205303_at 3764 KCNJ8 potassium inwardly‐rectifying channel, subfamily J, member 8 5,68 6,87 0,00 226841_at 219972 MPEG1 macrophage expressed gene 1 5,59 3,76 0,00 203923_s_at 1536 CYBB cytochrome b‐245, beta polypeptide (chronic granulomatous disease) 5,58 4,70 0,00 210135_s_at 6474 SHOX2 short stature homeobox 2 5,53 5,58 0,00 1562642_at ‐‐ ‐‐ ‐‐ 5,42 5,03 0,00 242605_at 1634 DCN decorin 5,23 3,92 0,00 228750_at ‐‐ ‐‐ ‐‐ 5,21 7,22 0,00 collagen, type III, alpha 1 (Ehlers‐Danlos syndrome type IV, autosomal 201852_x_at 1281 COL3A1 dominant) 5,10 8,46 0,00 3493///3 IGHA1///IGHA immunoglobulin heavy constant alpha 1///immunoglobulin heavy 217022_s_at 494 2 constant alpha 2 (A2m marker) 5,07 9,53 0,00 1 202311_s_at 1277 COL1A1 collagen, type I, alpha 1 5,07 10,41 0,00 1559889_at 440686 HIST2H3PS2 histone cluster 2, H3, pseudogene 2 5,03 3,81 0,00 collagen, type III, alpha 1 (Ehlers‐Danlos syndrome type IV, autosomal 215076_s_at 1281 COL3A1 dominant) 4,99 9,46 0,00 34210_at 1043 CD52 CD52 molecule 4,96 13,53 0,00 1552701_a_a t 114769 COP1 caspase‐1 dominant‐negative inhibitor pseudo‐ICE 4,93 3,47 0,00 212865_s_at 7373 COL14A1 collagen, type XIV, alpha 1 (undulin) 4,90 8,32 0,00 226311_at 9509 ADAMTS2 ADAM metallopeptidase with thrombospondin type 1 motif, 2 4,88 5,01 0,00 1556499_s_at 1277 COL1A1 collagen, type I, alpha 1 4,88 5,88 0,00 212067_s_at 715 C1R complement component 1, r subcomponent 4,87 2,94 0,00 204162_at 10403 NDC80 NDC80 homolog, kinetochore complex component (S. cerevisiae) 4,85 7,87 0,00 1558834_s_at 254268 C1orf62 chromosome 1 open reading frame 62 4,84 4,73 0,00 201645_at 3371 TNC tenascin C (hexabrachion) 4,83 5,13 0,00 208747_s_at 716 C1S complement component 1, s subcomponent 4,78 4,90 0,00 collagen, type III, alpha 1 (Ehlers‐Danlos syndrome type IV, autosomal 211161_s_at 1281 COL3A1 dominant) 4,76 4,28 0,00 204829_s_at 2350 FOLR2 folate receptor 2 (fetal) 4,75 3,29 0,00 216575_at ‐‐ ‐‐ ‐‐ 4,71 3,16 0,00 205987_at 911 CD1C CD1c molecule 4,69 4,58 0,00 1563074_at 255654 LOC255654 hypothetical protein LOC255654 4,58 5,36 0,27 1562111_at 9577 BRE brain and reproductive organ‐expressed (TNFRSF1A modulator) 4,58 5,22 0,27 242878_at ‐‐ ‐‐ ‐‐ 4,57 2,61 0,27 202404_s_at 1278 COL1A2 collagen, type I, alpha 2 4,55 11,25 0,27 205484_at 27240 SIT1 signaling threshold regulating transmembrane adaptor 1 4,53 14,50 0,27 206392_s_at 5918 RARRES1 retinoic acid receptor responder (tazarotene induced) 1 4,52 3,99 0,27 224964_s_at 54331 GNG2 guanine nucleotide binding protein (G protein), gamma 2 4,52 3,00 0,27 209869_at 150 ADRA2A adrenergic, alpha‐2A‐, receptor 4,51 9,88 0,27 2 202310_s_at 1277 COL1A1 collagen, type I, alpha 1 4,49 5,16 0,27 233633_at 79718 TBL1XR1 transducin (beta)‐like 1X‐linked receptor 1 4,49 3,35 0,27 solute carrier family 1 (glutamate/neutral amino acid transporter), 244377_at 6509 SLC1A4 member 4 4,48 3,08 0,27 1566161_at 4212 MEIS2 Meis homeobox 2 4,47 4,30 0,27 1561564_at ‐‐ ‐‐ ‐‐ 4,44 4,35 0,27 222838_at 57823 SLAMF7 SLAM family member 7 4,42 10,33 0,35 229391_s_at 441168 FAM26F family with sequence similarity 26, member F 4,40 9,62 0,35 238408_at 55074 OXR1 oxidation resistance 1 4,40 3,74 0,35 205859_at 9450 LY86 lymphocyte antigen 86 4,39 3,99 0,35 209708_at 26002 MOXD1 monooxygenase, DBH‐like 1 4,38 5,28 0,35 1561123_at 5396 PRRX1 paired related homeobox 1 4,37 9,47 0,35 222895_s_at 64919 BCL11B B‐cell CLL/lymphoma 11B (zinc finger protein) 4,37 3,82 0,35 210629_x_at 7940 LST1 leukocyte specific transcript 1 4,36 8,02 0,35 234248_at ‐‐ ‐‐ ‐‐ 4,36 3,80 0,35 217147_s_at 50852 TRAT1 T cell receptor associated transmembrane adaptor 1 4,36 6,96 0,35 228372_at 170371 C10orf128 chromosome 10 open reading frame 128 4,33 3,77 0,35 219519_s_at 6614 SIGLEC1 sialic acid binding Ig‐like lectin 1, sialoadhesin 4,32 4,50 0,35 1569755_at ‐‐ ‐‐ ‐‐ 4,32 3,88 0,35 219528_s_at 64919 BCL11B B‐cell CLL/lymphoma 11B (zinc finger protein) 4,32 8,63 0,35 238529_at 8370 HIST2H4A histone cluster 2, H4a 4,31 4,56 0,35 244125_at 403340 MGC70870 hypothetical LOC403340 4,30 5,95 0,35 232645_at 153684 LOC153684 hypothetical protein LOC153684 4,29 4,08 0,35 219815_at 79690 GAL3ST4 galactose‐3‐O‐sulfotransferase 4 4,28 4,99 0,35 204205_at 60489 APOBEC3G apolipoprotein B mRNA editing enzyme, catalytic polypeptide‐like 3G 4,28 3,44 0,35 221731_x_at 1462 VCAN versican 4,28 8,11 0,35 243819_at 54331 GNG2 guanine nucleotide binding protein (G protein), gamma 2 4,27 4,47 0,35 3 1555852_at ‐‐ ‐‐ ‐‐ 4,26 3,22 0,35 1556516_at ‐‐ ‐‐ ‐‐ 4,26 2,85 0,35 239963_at ‐‐ ‐‐ ‐‐ 4,26 2,80 0,35 205872_x_at 9659 PDE4DIP phosphodiesterase 4D interacting protein (myomegalin) 4,26 5,03 0,35 204620_s_at 1462 VCAN versican 4,24 5,17 0,35 211881_x_at 28831 IGLJ3 immunoglobulin lambda joining 3 4,23 4,58 0,35 220146_at 51284 TLR7 toll‐like receptor 7 4,23 7,80 0,35 240988_x_at ‐‐ ‐‐ ‐‐ 4,22 6,82 0,35 1561926_at ‐‐ ‐‐ ‐‐ 4,22 5,39 0,35 204661_at 1043 CD52 CD52 molecule 4,22 12,70 0,35 1559289_at ‐‐ ‐‐ ‐‐ 4,20 8,71 0,35 224418_x_at 5369 PMCHL1 pro‐melanin‐concentrating hormone‐like 1 4,18 2,93 0,35 proteasome (prosome, macropain) subunit, beta type, 9 (large 204279_at 5698 PSMB9 multifunctional peptidase 2) 4,18 4,56 0,35 202947_s_at 2995 GYPC glycophorin C (Gerbich blood group) 4,17 2,94 0,35 226789_at ‐‐ ‐‐ ‐‐ 4,17 2,42 0,35 1564391_at 5825 ABCD3 ATP‐binding cassette, sub‐family D (ALD), member 3 4,17 3,47 0,35 237117_at ‐‐ ‐‐ ‐‐ 4,17 4,17 0,35 244042_x_at ‐‐ ‐‐ ‐‐ 4,16 10,39 0,35 219666_at 64231 MS4A6A membrane‐spanning 4‐domains, subfamily A, member 6A 4,15 4,99 0,35 206960_at 2846 GPR23 G protein‐coupled receptor 23 4,15 3,64 0,35 244605_at 2043 EPHA4 EPH receptor A4 4,14 5,14 0,35 1559696_at ‐‐ ‐‐ ‐‐ 4,13 5,74 0,35 225655_at 29128 UHRF1 ubiquitin‐like, containing PHD and RING finger domains, 1 4,12 3,24 0,35 225897_at 4082 MARCKS myristoylated alanine‐rich protein kinase C substrate 4,11 2,62 0,52 216193_at 440366 LOC440366 hect domain and RLD 2 pseudogene 4,09 11,32 0,52 214181_x_at 7940 LST1 leukocyte specific transcript 1 4,09 3,84 0,52 1564259_at 9099 USP2 ubiquitin specific peptidase 2 4,08 2,66 0,52 4 240890_at ‐‐ ‐‐ ‐‐ 4,08 2,59 0,52 205943_at 6999 TDO2 tryptophan 2,3‐dioxygenase 4,07 4,92 0,52 229968_at ‐‐ ‐‐ ‐‐ 4,05 3,97 0,52 225975_at 54510 PCDH18 protocadherin 18 4,04 4,47 0,52 242232_at 149401 LOC149401 hypothetical protein LOC149401 4,04 4,34 0,52 202953_at 713 C1QB complement component 1, q subcomponent, B chain 4,04 8,66 0,52 201048_x_at 5870 RAB6A RAB6A, member RAS oncogene family 4,04 1,97 0,52 proteasome (prosome, macropain) subunit, beta type, 8 (large 209040_s_at 5696 PSMB8 multifunctional peptidase 7) 4,03 3,11 0,52 225016_at 147495 APCDD1 adenomatosis polyposis coli down‐regulated 1 4,03 4,13 0,52 241945_at ‐‐ ‐‐ ‐‐ 4,03 2,50 0,52 1559697_a_a t ‐‐ ‐‐ ‐‐ 4,03 3,16 0,52 234203_at 9215 LARGE like‐glycosyltransferase 4,02 5,60 0,52 223922_x_at 64231 MS4A6A membrane‐spanning 4‐domains, subfamily A, member 6A 4,01 4,79 0,52 1554899_s_at 2207 FCER1G Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide 4,01 4,95 0,52 234179_at 313 AOAH acyloxyacyl hydrolase (neutrophil) 4,00 3,96 0,52 208119_s_at 81931 ZNF93 zinc finger protein 93 3,99 9,45 0,52 441519// /441520/ RP13‐ //441521 36C9.3///CT45 ///54146 ‐4///RP13‐ cancer/testis antigen CT45‐3///cancer/testis antigen CT45‐ 5///5414 36C9.6///CT45 4///cancer/testis antigen CT45‐5///cancer/testis antigen CT45‐ 235700_at 66 ‐6///CT45‐1 6///cancer/testis antigen CT45‐1 3,99 6,70 0,52 208235_x_at 2579 GAGE7 G antigen 7 3,99 14,39 0,52 233861_at ‐‐ ‐‐ ‐‐ 3,98 5,52 0,52 205381_at 10234 LRRC17 leucine rich repeat containing 17 3,97 2,43 0,52 243986_at 144766 LOC144766 hypothetical protein LOC144766 3,97 4,47 0,52 222940_at 6783 SULT1E1 sulfotransferase family 1E, estrogen‐preferring, member 1 3,96 2,05 0,52 5 223280_x_at 64231 MS4A6A membrane‐spanning 4‐domains, subfamily A, member 6A 3,96 4,37 0,52 1562223_at ‐‐ ‐‐ ‐‐ 3,96 16,84 0,52 232458_at ‐‐ ‐‐ ‐‐ 3,95 3,29 0,52 228094_at 120425 AMICA1 adhesion molecule, interacts with CXADR antigen 1 3,95 11,70 0,52 1559170_at ‐‐ ‐‐ ‐‐ 3,95 4,14 0,52 233815_at 10003 NAALAD2 N‐acetylated alpha‐linked acidic dipeptidase 2 3,95 2,54 0,52 217478_s_at 3108 HLA‐DMA major histocompatibility complex, class II, DM alpha 3,95 2,56 0,52 244348_at ‐‐ ‐‐ ‐‐ 3,95 2,65 0,52 1562992_at 79846 FLJ21062 hypothetical protein FLJ21062 3,94 5,69 0,52 210176_at 7096 TLR1 toll‐like receptor 1 3,94 1,92 0,52 223930_at ‐‐ ‐‐ ‐‐ 3,93 6,70 0,52 224006_at ‐‐ ‐‐ ‐‐ 3,92 4,40 0,52 244061_at 55843 ARHGAP15 Rho GTPase activating protein 15 3,92 4,77 0,52 240734_at ‐‐ ‐‐ ‐‐ 3,91 7,33 0,52 242491_at ‐‐ ‐‐ ‐‐ 3,91 6,71 0,52 206497_at 55744 C7orf44 chromosome 7 open reading frame 44 3,91 4,59 0,52 1552908_at 148823 C1orf150 chromosome 1 open reading
Load more

Recommended publications
  • C19) United States C12) Patent Application Publication C10) Pub
    1111111111111111 IIIIII IIIII 1111111111 11111 11111 111111111111111 1111111111 1111111111 11111111 US 20200081016Al c19) United States c12) Patent Application Publication c10) Pub. No.: US 2020/0081016 Al Talaat et al. (43) Pub. Date: Mar. 12, 2020 (54) BIOMARKERS FOR EARLY DIAGNOSIS Publication Classification AND DIFFERENTIATION OF (51) Int. Cl. MYCOBACTERIAL INFECTION GOIN 33/68 (2006.01) C12Q 116851 (2006.01) (71) Applicant: Wisconsin Alumni Research GOIN 33/569 (2006.01) Foundation, Madison, WI (US) (52) U.S. Cl. (72) Inventors: Adel Mohamed Talaat, Madison, WI CPC ......... GOIN 33/6854 (2013.01); GOIN 33/68 (US); Chia-wei Wu, Madison, WI (US) (2013.01); GOIN 2800/50 (2013.01); GOIN 33/5695 (2013.01); GOIN 2800/26 (2013.01); (21) Appl. No.: 16/555,819 C12Q 116851 (2013.01) (22) Filed: Aug. 29, 2019 (57) ABSTRACT Mycobacterial-specific biomarkers and methods of using Related U.S. Application Data such biomarkers for diagnosis of mycobacterial infection in (60) Provisional application No. 62/728,387, filed on Sep. a mammal are disclosed. 7, 2018. Specification includes a Sequence Listing. Patent Application Publication Mar. 12, 2020 Sheet 1 of 10 US 2020/0081016 Al FIG. 1 ·~{:: -{t i * !lpNbiNi$ 1 !lpN p~ra 111:111111 llillllll: 111!11,111llltllllll~ 11111 ■111 ~; C,,Nmnsus KR.IGINMTKX L.lC(X.AXXXXG AXXXXMPXTX RXO-GXVXXVG VKVXPWIPTX ® • ® l I I iipN lK>V(S ~Hl!lli!Wiofflij 1!11.llofJiillj mllB~lijftlt flol=fiolill ••t-il-~MM ~9 llpN p~ra HfHJoffit:torti ilffllGNillm miJllt~ttiollf ~•01:101111 llm:l:l1IA@~ iOO C,,nstmsus XXRXLXXGRS Vt IOGNT.LDP i LOt.MLSXXR XXGXOG.I...XVO ODXXXSR:AXM t2:;: i-/4~~ ! l 1 I~~~~b;:: llllil~l:1:1 llil 111111:1~:111~ 1111111::;1 1lllilllll: ~:~ C,,nimnsus XXXXXXXPGP QtHVDVXXI...X XPGPAGXIPA RHYRPXGGXX QXPt.l...VFYHG Consl:lrvat,ofl -:§;::.
    [Show full text]
  • Peking University-Juntendo University Joint Symposium on Cancer Research and Treatment ADAM28 (A Disintegrin and Metalloproteinase 28) in Cancer Cell Proliferation and Progression
    Whatʼs New from Juntendo University, Tokyo Juntendo Medical Journal 2017. 63(5), 322-325 Peking University - Juntendo University Joint Symposium on Cancer Research and Treatment ADAM28 (a Disintegrin and Metalloproteinase 28) in Cancer Cell Proliferation and Progression YASUNORI OKADA＊ ＊Department of Pathophysiology for Locomotive and Neoplastic Diseases, Juntendo University Graduate School of Medicine, Tokyo, Japan A disintegrinandmetalloproteinase 28 (ADAM28) is overexpressedpredominantlyby carcinoma cells in more than 70% of the non-small cell lung carcinomas, showing positive correlations with carcinoma cell proliferation and metastasis. ADAM28 cleaves insulin-like growth factor binding protein-3 (IGFBP-3) in the IGF-I/IGFBP-3 complex, leading to stimulation of cell proliferation by intact IGF-I released from the complex. ADAM28 also degrades von Willebrand factor (VWF), which induces apoptosis in human carcinoma cell lines with negligible ADAM28 expression, andthe VWF digestionby ADAM28-expressing carcinoma cells facilitates them to escape from VWF-induced apoptosis, resulting in promotion of metastasis. We have developed human antibodies against ADAM28 andshown that one of them significantly inhibits tumor growth andmetastasis using lung adenocarcinoma cells. Our data suggest that ADAM28 may be a new molecular target for therapy of the patients with ADAM28-expressing non-small cell lung carcinoma. Key words: a disintegrin and metalloproteinase 28 (ADAM28), cell proliferation, invasion, metastasis, human antibody inhibitor Introduction human cancers 2). However, development of the synthetic inhibitors of MMPs andtheir application Cancer cell proliferation andprogression are for treatment of the cancer patients failed 3). modulated by proteolytic cleavage of tissue micro- On the other hand, members of the ADAM (a environmental factors such as extracellular matrix disintegrin and metalloproteinase) gene family, (ECM), growth factors andcytokines, receptors another family belonging to the metzincin gene andcell adhesionmolecules.
    [Show full text]
  • Enzymatic Encoding Methods for Efficient Synthesis Of
    (19) TZZ__T (11) EP 1 957 644 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.: of the grant of the patent: C12N 15/10 (2006.01) C12Q 1/68 (2006.01) 01.12.2010 Bulletin 2010/48 C40B 40/06 (2006.01) C40B 50/06 (2006.01) (21) Application number: 06818144.5 (86) International application number: PCT/DK2006/000685 (22) Date of filing: 01.12.2006 (87) International publication number: WO 2007/062664 (07.06.2007 Gazette 2007/23) (54) ENZYMATIC ENCODING METHODS FOR EFFICIENT SYNTHESIS OF LARGE LIBRARIES ENZYMVERMITTELNDE KODIERUNGSMETHODEN FÜR EINE EFFIZIENTE SYNTHESE VON GROSSEN BIBLIOTHEKEN PROCEDES DE CODAGE ENZYMATIQUE DESTINES A LA SYNTHESE EFFICACE DE BIBLIOTHEQUES IMPORTANTES (84) Designated Contracting States: • GOLDBECH, Anne AT BE BG CH CY CZ DE DK EE ES FI FR GB GR DK-2200 Copenhagen N (DK) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • DE LEON, Daen SK TR DK-2300 Copenhagen S (DK) Designated Extension States: • KALDOR, Ditte Kievsmose AL BA HR MK RS DK-2880 Bagsvaerd (DK) • SLØK, Frank Abilgaard (30) Priority: 01.12.2005 DK 200501704 DK-3450 Allerød (DK) 02.12.2005 US 741490 P • HUSEMOEN, Birgitte Nystrup DK-2500 Valby (DK) (43) Date of publication of application: • DOLBERG, Johannes 20.08.2008 Bulletin 2008/34 DK-1674 Copenhagen V (DK) • JENSEN, Kim Birkebæk (73) Proprietor: Nuevolution A/S DK-2610 Rødovre (DK) 2100 Copenhagen 0 (DK) • PETERSEN, Lene DK-2100 Copenhagen Ø (DK) (72) Inventors: • NØRREGAARD-MADSEN, Mads • FRANCH, Thomas DK-3460 Birkerød (DK) DK-3070 Snekkersten (DK) • GODSKESEN,
    [Show full text]
  • Beta-Arrestin-Mediated Signaling in the Heart
    SPECIAL ARTICLE Circ J 2008; 72: 1725–1729 Beta-Arrestin-Mediated Signaling in the Heart Priyesh A. Patel, BS; Douglas G. Tilley, PhD*; Howard A. Rockman, MD*,** Beta-arrestin is a multifunctional adapter protein well known for its role in G-protein-coupled receptor (GPCR) desensitization. Exciting new evidence indicates thatβ-arrestin is also a signaling molecule capable of initiating its own G-protein-independent signaling at GPCRs. One of the best-studiedβ-arrestin signaling pathways is the one involvingβ-arrestin-dependent activation of a mitogen-activated protein kinase cascade, the extracellular regulated kinase (ERK). ERK signaling, which is classically activated by agonist stimulation of the epidermal growth factor receptor (EGFR), can be activated by a number of GPCRs in aβ-arrestin-dependent manner. Recent work in animal models of heart failure suggests thatβ-arrestin-dependent activation of EGFR/ERK signaling by theβ-1-adrenergic receptor, and possibly the angiotensin II Type 1A receptor, are cardioprotective. Hence, a new model of signaling at cardiac GPCRs has emerged and implicates classical G-protein-mediated signaling with promoting harmful remodeling in heart failure, while concurrently linkingβ-arrestin-dependent, G-protein-inde- pendent signaling with cardioprotective effects. Based on this paradigm, a new class of drugs could be identified, termed “biased ligands”, which simultaneously block harmful G-protein signaling, while also promoting cardio- protectiveβ-arrestin-dependent signaling, leading to a potential breakthrough
    [Show full text]
  • BMC Evolutionary Biology Biomed Central
    BMC Evolutionary Biology BioMed Central Research article Open Access On the origins of arrestin and rhodopsin Carlos E Alvarez1,2,3 Address: 1Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA, 2Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43210, USA and 3Novartis Institutes of BioMedical Research, CH-4002 Basel, Switzerland Email: Carlos E Alvarez - [email protected] Published: 29 July 2008 Received: 11 January 2008 Accepted: 29 July 2008 BMC Evolutionary Biology 2008, 8:222 doi:10.1186/1471-2148-8-222 This article is available from: http://www.biomedcentral.com/1471-2148/8/222 © 2008 Alvarez; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: G protein coupled receptors (GPCRs) are the most numerous proteins in mammalian genomes, and the most common targets of clinical drugs. However, their evolution remains enigmatic. GPCRs are intimately associated with trimeric G proteins, G protein receptor kinases, and arrestins. We conducted phylogenetic studies to reconstruct the history of arrestins. Those findings, in turn, led us to investigate the origin of the photosensory GPCR rhodopsin. Results: We found that the arrestin clan is comprised of the Spo0M protein family in archaea and bacteria, and the arrestin and Vps26 families in eukaryotes. The previously known animal arrestins are members of the visual/beta subfamily, which branched from the founding "alpha" arrestins relatively recently.
    [Show full text]
  • An Animal Model with a Cardiomyocyte-Specific Deletion of Estrogen Receptor Alpha: Functional, Metabolic, and Differential Netwo
    Washington University School of Medicine Digital Commons@Becker Open Access Publications 2014 An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: Functional, metabolic, and differential network analysis Sriram Devanathan Washington University School of Medicine in St. Louis Timothy Whitehead Washington University School of Medicine in St. Louis George G. Schweitzer Washington University School of Medicine in St. Louis Nicole Fettig Washington University School of Medicine in St. Louis Attila Kovacs Washington University School of Medicine in St. Louis See next page for additional authors Follow this and additional works at: https://digitalcommons.wustl.edu/open_access_pubs Recommended Citation Devanathan, Sriram; Whitehead, Timothy; Schweitzer, George G.; Fettig, Nicole; Kovacs, Attila; Korach, Kenneth S.; Finck, Brian N.; and Shoghi, Kooresh I., ,"An animal model with a cardiomyocyte-specific deletion of estrogen receptor alpha: Functional, metabolic, and differential network analysis." PLoS One.9,7. e101900. (2014). https://digitalcommons.wustl.edu/open_access_pubs/3326 This Open Access Publication is brought to you for free and open access by Digital Commons@Becker. It has been accepted for inclusion in Open Access Publications by an authorized administrator of Digital Commons@Becker. For more information, please contact [email protected]. Authors Sriram Devanathan, Timothy Whitehead, George G. Schweitzer, Nicole Fettig, Attila Kovacs, Kenneth S. Korach, Brian N. Finck, and Kooresh I. Shoghi This open access publication is available at Digital Commons@Becker: https://digitalcommons.wustl.edu/open_access_pubs/3326 An Animal Model with a Cardiomyocyte-Specific Deletion of Estrogen Receptor Alpha: Functional, Metabolic, and Differential Network Analysis Sriram Devanathan1, Timothy Whitehead1, George G. Schweitzer2, Nicole Fettig1, Attila Kovacs3, Kenneth S.
    [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]
  • Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
    Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491
    [Show full text]
  • To Study Mutant P53 Gain of Function, Various Tumor-Derived P53 Mutants
    Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science By Shama K Khokhar M.Sc., Bilaspur University, 2004 B.Sc., Bhopal University, 2002 2007 1 COPYRIGHT SHAMA K KHOKHAR 2007 2 WRIGHT STATE UNIVERSITY SCHOOL OF GRADUATE STUDIES Date of Defense: 12-03-07 I HEREBY RECOMMEND THAT THE THESIS PREPARED UNDER MY SUPERVISION BY SHAMA KHAN KHOKHAR ENTITLED Differential effects of mutant TAp63γ on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression BE ACCEPTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF Master of Science Madhavi P. Kadakia, Ph.D. Thesis Director Daniel Organisciak , Ph.D. Department Chair Committee on Final Examination Madhavi P. Kadakia, Ph.D. Steven J. Berberich, Ph.D. Michael Leffak, Ph.D. Joseph F. Thomas, Jr., Ph.D. Dean, School of Graduate Studies 3 Abstract Khokhar, Shama K. M.S., Department of Biochemistry and Molecular Biology, Wright State University, 2007 Differential effect of TAp63γ mutants on transactivation of p53 and/or p63 responsive genes and their effects on global gene expression. p63, a member of the p53 gene family, known to play a role in development, has more recently also been implicated in cancer progression. Mice lacking p63 exhibit severe developmental defects such as limb truncations, abnormal skin, and absence of hair follicles, teeth, and mammary glands. Germline missense mutations of p63 have been shown to be responsible for several human developmental syndromes including SHFM, EEC and ADULT syndromes and are associated with anomalies in the development of organs of epithelial origin.
    [Show full text]
  • Ingenuity Pathway Analysis of Differentially Expressed Genes Involved in Signaling Pathways and Molecular Networks in Rhoe Gene‑Edited Cardiomyocytes
    INTERNATIONAL JOURNAL OF MOleCular meDICine 46: 1225-1238, 2020 Ingenuity pathway analysis of differentially expressed genes involved in signaling pathways and molecular networks in RhoE gene‑edited cardiomyocytes ZHONGMING SHAO1*, KEKE WANG1*, SHUYA ZHANG2, JIANLING YUAN1, XIAOMING LIAO1, CAIXIA WU1, YUAN ZOU1, YANPING HA1, ZHIHUA SHEN1, JUNLI GUO2 and WEI JIE1,2 1Department of Pathology, School of Basic Medicine Sciences, Guangdong Medical University, Zhanjiang, Guangdong 524023; 2Hainan Provincial Key Laboratory for Tropical Cardiovascular Diseases Research and Key Laboratory of Emergency and Trauma of Ministry of Education, Institute of Cardiovascular Research of The First Affiliated Hospital, Hainan Medical University, Haikou, Hainan 571199, P.R. China Received January 7, 2020; Accepted May 20, 2020 DOI: 10.3892/ijmm.2020.4661 Abstract. RhoE/Rnd3 is an atypical member of the Rho super- injury and abnormalities, cell‑to‑cell signaling and interaction, family of proteins, However, the global biological function and molecular transport. In addition, 885 upstream regulators profile of this protein remains unsolved. In the present study, a were enriched, including 59 molecules that were predicated RhoE‑knockout H9C2 cardiomyocyte cell line was established to be strongly activated (Z‑score >2) and 60 molecules that using CRISPR/Cas9 technology, following which differentially were predicated to be significantly inhibited (Z‑scores <‑2). In expressed genes (DEGs) between the knockout and wild‑type particular, 33 regulatory effects and 25 networks were revealed cell lines were screened using whole genome expression gene to be associated with the DEGs. Among them, the most signifi- chips. A total of 829 DEGs, including 417 upregulated and cant regulatory effects were ‘adhesion of endothelial cells’ and 412 downregulated, were identified using the threshold of ‘recruitment of myeloid cells’ and the top network was ‘neuro- fold changes ≥1.2 and P<0.05.
    [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]
  • Pancancer Progression Human Vjune2017
    Gene Symbol Accession Alias/Prev Symbol Official Full Name AAMP NM_001087.3 - angio-associated, migratory cell protein ABI3BP NM_015429.3 NESHBP|TARSH ABI family, member 3 (NESH) binding protein ACHE NM_000665.3 ACEE|ARACHE|N-ACHE|YT acetylcholinesterase ACTG2 NM_001615.3 ACT|ACTA3|ACTE|ACTL3|ACTSG actin, gamma 2, smooth muscle, enteric ACVR1 NM_001105.2 ACTRI|ACVR1A|ACVRLK2|ALK2|FOP|SKR1|TSRI activin A receptor, type I ACVR1C NM_145259.2 ACVRLK7|ALK7 activin A receptor, type IC ACVRL1 NM_000020.1 ACVRLK1|ALK-1|ALK1|HHT|HHT2|ORW2|SKR3|TSR-I activin A receptor type II-like 1 ADAM15 NM_207195.1 MDC15 ADAM metallopeptidase domain 15 ADAM17 NM_003183.4 ADAM18|CD156B|CSVP|NISBD|TACE ADAM metallopeptidase domain 17 ADAM28 NM_014265.4 ADAM 28|ADAM23|MDC-L|MDC-Lm|MDC-Ls|MDCL|eMDC II|eMDCII ADAM metallopeptidase domain 28 ADAM8 NM_001109.4 CD156|MS2 ADAM metallopeptidase domain 8 ADAM9 NM_001005845.1 CORD9|MCMP|MDC9|Mltng ADAM metallopeptidase domain 9 ADAMTS1 NM_006988.3 C3-C5|METH1 ADAM metallopeptidase with thrombospondin type 1 motif, 1 ADAMTS12 NM_030955.2 PRO4389 ADAM metallopeptidase with thrombospondin type 1 motif, 12 ADAMTS8 NM_007037.4 ADAM-TS8|METH2 ADAM metallopeptidase with thrombospondin type 1 motif, 8 ADAP1 NM_006869.2 CENTA1|GCS1L|p42IP4 ArfGAP with dual PH domains 1 ADD1 NM_001119.4 ADDA adducin 1 (alpha) ADM2 NM_001253845.1 AM2|dJ579N16.4 adrenomedullin 2 ADRA2B NM_000682.4 ADRA2L1|ADRA2RL1|ADRARL1|ALPHA2BAR|alpha-2BAR adrenoceptor alpha 2B AEBP1 NM_001129.3 ACLP AE binding protein 1 AGGF1 NM_018046.3 GPATC7|GPATCH7|HSU84971|HUS84971|VG5Q
    [Show full text]