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Supplementary Table 1 - Transcriptomics Analysis

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Supplementary Table 1 - Transcriptomics analysis Gene mean lower CI upper CI mean lower CI upper CI pval regulation Control Control Control CKD5 CKD5 CKD5 TAX1BP3 166 145 188 127 110 145 0.000025249 DOWN LOC10012869 1147 878 1416 1585 1331 1838 0.000055095 UP LOC728711 219 169 268 295 244 347 0.000147349 UP CHRM2 456 281 631 752 539 965 0.000160221 UP TUFM 249 202 296 186 144 229 0.000275465 DOWN LOC10013356 1757 1336 2178 2381 1908 2853 0.000317399 UP GART 252 197 307 369 268 470 0.000337589 UP ACTG1 3496 2862 4129 2553 1821 3286 0.000358633 DOWN C19ORF12 756 482 1031 1169 846 1492 0.000364414 UP EPHA3 198 153 243 319 206 432 0.000424626 UP CALU 368 251 485 236 149 322 0.000453493 DOWN ZMAT5 304 188 420 505 330 681 0.000486754 UP CALM2 1675 1414 1935 1251 880 1622 0.000565783 DOWN CUEDC2 267 195 339 195 156 235 0.000566311 DOWN MGP 1963 1433 2493 1213 589 1837 0.000596141 DOWN CCNB1IP1 1056 818 1293 1561 1083 2038 0.000602318 UP EIF3I 457 386 527 328 210 446 0.000626151 DOWN GNPTAB 749 412 1086 1177 833 1522 0.000690099 UP RPL10A 1221 772 1669 722 355 1089 0.000773455 DOWN DOPEY2 250 151 349 394 267 522 0.000774827 UP AP3M1 773 506 1040 1163 816 1510 0.00078137 UP LOC439953 1357 1133 1580 979 624 1334 0.000806034 DOWN LOC728624 1153 694 1613 1753 1245 2262 0.000817567 UP STAP2 726 429 1023 1092 792 1392 0.000827991 UP RPLP1 1581 1414 1748 1234 888 1579 0.000853525 DOWN LOC654096 273 168 379 174 117 232 0.000855063 DOWN LOC10013377 1250 720 1780 1794 1419 2170 0.000862097 UP RARRES3 497 378 617 341 203 480 0.00102823 DOWN SLC44A4 586 302 870 1017 606 1428 0.001073943 UP PODXL 998 576 1421 1506 1071 1941 0.001095301 UP B2M 1758 1233 2283 1280 989 1570 0.001099624 DOWN LOC10013082 1607 1069 2146 2200 1724 2676 0.001115864 UP SORBS1 235 169 301 413 223 604 0.001142018 UP LOC646200 1923 1602 2244 1510 1138 1882 0.00114479 DOWN FGD2 394 258 530 602 400 804 0.001157249 UP FKSG44 359 240 479 587 354 820 0.001162975 UP CD151 408 291 524 254 114 395 0.001177407 DOWN G6PD 177 138 216 139 120 157 0.001217668 DOWN LOC10013251 1160 791 1530 1565 1234 1896 0.001219375 UP PACRGL 389 240 537 628 389 867 0.001254797 UP C6ORF48 1236 749 1724 1785 1320 2250 0.001288221 UP BAX 1862 1242 2483 2560 1968 3153 0.00130583 UP MTHFD2 749 448 1050 1155 769 1541 0.001352148 UP C1ORF84 213 145 281 310 215 404 0.001383865 UP FBXW11 249 217 281 186 127 245 0.001401546 DOWN LOC729629 374 228 521 568 384 753 0.001402721 UP PI16 444 291 597 287 161 412 0.001407685 DOWN TMED7 214 158 270 160 119 200 0.001416159 DOWN ZNF765 914 616 1213 1251 958 1544 0.001429471 UP RPE 645 351 939 1025 664 1387 0.001453228 UP ZMYM6 582 371 794 950 566 1334 0.001464595 UP IGFBP6 506 222 789 276 165 388 0.001484047 DOWN ZC3HAV1L 561 409 714 818 551 1084 0.001492427 UP LOC10012885 1079 543 1616 1668 1160 2177 0.001494742 UP FKTN 1610 1032 2189 2228 1703 2753 0.001550957 UP TERF1 318 217 419 441 325 558 0.00168211 UP OLFML2A 188 140 235 139 98 180 0.001724762 DOWN LOC10013276 509 334 683 759 501 1017 0.001811432 UP ZNF568 233 158 308 329 234 423 0.001812475 UP PNPT1 1433 950 1916 1954 1486 2421 0.001873828 UP MARCH8 1095 645 1546 1599 1133 2064 0.00191015 UP VAMP5 216 185 247 170 123 218 0.001926109 DOWN TMEM176B 163 137 189 125 100 150 0.00193535 DOWN LOC646996 686 450 922 1027 671 1383 0.001942541 UP EIF3L 582 488 676 460 337 583 0.001946074 DOWN MTFMT 346 237 455 489 344 635 0.001991067 UP DKFZP779L18 465 369 561 644 443 844 0.002078011 UP LOC10013022 973 668 1279 1419 945 1893 0.002107921 UP RAD51 150 115 186 240 136 345 0.002119693 UP LOC10013005 1120 623 1617 1670 1152 2188 0.002119889 UP ZNF669 258 172 343 455 225 685 0.002214271 UP AHNAK 2104 1840 2369 1794 1486 2103 0.00234022 DOWN KARS 592 527 657 475 342 608 0.002399857 DOWN EIF3M 371 336 406 318 260 376 0.002440115 DOWN VPS41 310 150 471 508 303 713 0.002519827 UP DYNLRB1 363 289 437 285 211 359 0.002522983 DOWN LOC650843 1185 902 1469 1535 1170 1900 0.002572228 UP LOC728073 259 160 359 415 240 591 0.002618235 UP WDR23 458 227 689 790 423 1156 0.002629141 UP LOC400721 766 402 1131 1175 766 1584 0.00264846 UP MGP 1196 256 2135 457 -20 933 0.002654472 DOWN TGOLN2 440 278 603 300 190 410 0.002665815 DOWN LOC644934 790 437 1143 463 183 744 0.002669022 DOWN RPS27L 295 175 415 436 290 582 0.002699767 UP EIF2AK4 826 513 1139 1218 803 1633 0.002702012 UP IGBP1 248 183 312 187 133 241 0.002706663 DOWN ST20 1498 862 2134 2098 1569 2627 0.002710784 UP EPSTI1 258 196 321 153 56 250 0.00278045 DOWN ACBD7 388 181 595 664 363 966 0.002805533 UP SEPN1 427 268 586 672 393 951 0.002821417 UP ZNF100 336 224 448 490 319 661 0.002856561 UP LOC727808 1043 571 1514 1666 981 2352 0.002934665 UP DGCR6L 229 141 318 308 241 376 0.002948303 UP SNX3 334 255 414 259 190 328 0.003032518 DOWN LOC642267 152 114 189 217 140 294 0.003090311 UP FLJ20518 155 124 185 207 145 270 0.003095507 UP CFLAR 409 232 587 654 378 930 0.00310267 UP ZNF266 491 274 708 737 479 994 0.003151322 UP TES 1475 1078 1873 1876 1484 2268 0.003207634 UP HS.193557 211 163 260 164 119 209 0.003211711 DOWN LOC10013486 607 401 812 930 551 1309 0.003214956 UP MSTO2P 284 171 397 464 252 676 0.003217203 UP LOC10013417 604 372 836 902 571 1232 0.003276787 UP SLA2 470 273 666 686 459 914 0.003360203 UP C20ORF45 245 164 326 171 104 239 0.003375355 DOWN TAF8 859 428 1290 1249 898 1599 0.003378439 UP GSR 2318 1598 3037 2897 2450 3343 0.003450851 UP LOC10013044 331 199 463 539 292 786 0.00345406 UP LOC10012803 1760 1105 2414 2325 1838 2811 0.003475367 UP LOC642617 689 377 1001 979 708 1250 0.003514835 UP CD34 844 535 1153 580 356 805 0.003548855 DOWN LOC653314 1034 889 1180 812 549 1076 0.003579108 DOWN NDUFA11 314 183 445 209 127 291 0.003637738 DOWN LOC10013059 265 174 356 193 139 248 0.003647324 DOWN MFSD10 205 79 331 410 162 657 0.003708871 UP SEPHS2 260 231 289 205 137 273 0.003714217 DOWN AES 352 263 441 227 80 374 0.003799488 DOWN C15ORF63 306 204 408 459 275 643 0.003889114 UP FAU 1741 1426 2056 1273 710 1836 0.003961972 DOWN CPE 624 348 900 433 335 532 0.003980246 DOWN STAG3L1 615 473 758 831 570 1092 0.004022783 UP LPHN2 170 134 205 226 159 293 0.004033053 UP C6ORF145 285 227 343 216 139 294 0.004055318 DOWN PPIL5 257 170 345 419 216 622 0.004055721 UP PNPT1 1497 913 2081 2118 1450 2786 0.004087282 UP ZNF706 377 162 592 565 391 739 0.004126664 UP SLC16A12 1535 767 2302 2296 1510 3082 0.004146915 UP SC4MOL 493 292 694 674 501 847 0.004183362 UP RPS15A 5338 3299 7377 3506 1752 5260 0.004212937 DOWN DCN 1569 972 2167 1036 527 1545 0.004248647 DOWN RPS26P11 983 530 1437 567 158 976 0.004270952 DOWN PTGS1 281 223 338 200 107 293 0.004274666 DOWN RPL35A 2184 1541 2826 1503 764 2242 0.004299893 DOWN LOC10013262 4077 3316 4839 4671 4195 5147 0.004306162 UP FLJ32790 461 267 656 758 393 1124 0.004341789 UP C7ORF64 334 207 461 484 312 657 0.004404075 UP VIM 1694 1383 2005 1426 1176 1676 0.004421698 DOWN ZNHIT3 1265 865 1665 1777 1171 2383 0.004467841 UP C1ORF210 305 234 376 431 271 590 0.004483456 UP CHIC2 177 138 217 130 101 158 0.00448503 DOWN SLC30A6 298 174 422 431 284 578 0.004496768 UP ALKBH5 888 657 1120 674 458 890 0.004609562 DOWN LAPTM4B 739 616 863 481 145 817 0.004682915 DOWN PIGW 345 170 520 555 309 801 0.004705892 UP BCAS4 2218 1523 2914 2887 2188 3585 0.00470976 UP LOC10013171 277 223 331 391 242 539 0.004763983 UP LOC442609 274 130 417 472 229 714 0.004769077 UP LILRB1 985 647 1323 1372 926 1818 0.004778862 UP RCN2 214 159 269 170 133 208 0.004794232 DOWN TOP3A 180 146 215 290 142 438 0.00489167 UP AKAP12 209 155 263 157 107 208 0.004899763 DOWN PPFIBP1 373 218 527 527 359 695 0.004944701 UP LOC642210 1894 1053 2735 1270 787 1753 0.004954367 DOWN MRPL44 433 246 620 615 421 808 0.004979679 UP POT1 242 166 319 375 203 547 0.005004712 UP SPC24 254 171 338 389 217 560 0.005059289 UP LOC728054 238 117 358 395 203 587 0.005089242 UP RBP1 504 230 778 305 156 453 0.005091174 DOWN LEPR 365 205 526 248 160 337 0.005137255 DOWN IFIT2 253 150 355 169 92 246 0.005182105 DOWN CECR7 184 136 233 282 156 407 0.005235038 UP LOC10013010 564 481 647 672 540 804 0.005257856 UP FBLN1 1740 1015 2466 1164 647 1682 0.005331203 DOWN C8ORF37 728 426 1031 1093 654 1531 0.005362775 UP LOC728687 600 263 937 950 553 1347 0.005416208 UP AK3 626 489 764 427 175 680 0.005423325 DOWN ALG5 445 294 596 313 179 447 0.005476186 DOWN LOC10013462 1297 871 1723 1711 1257 2164 0.005505207 UP RAX2 345 161 528 539 314 764 0.005565887 UP LOC10013272 765 441 1090 1134 695 1573 0.00557166 UP GAR1 296 204 388 221 150 293 0.005643476 DOWN ARHGAP8 654 348 961 936 636 1236 0.005674981 UP SNTN 732 408 1055 1015 724 1306 0.00569236 UP LOC728991 1824 1142 2506 2407 1821 2993 0.005746029 UP PMVK 655 458 852 407 100 715 0.005784619 DOWN SERPING1 286 229 342 221 144 299 0.005799276 DOWN LOC285053 573 490 657 445 279 612 0.005812053 DOWN LOC10012827 437 284 590 650 379 920 0.005812564 UP CLTB 183 147 220 148 109 187 0.005886923 DOWN GYG2 248 170 325 342 225 459 0.0059211 UP FTHL7 1337 918 1756 926 462 1389 0.005953898 DOWN ZNF486 405 213 597 647 344 949 0.005993167 UP RNASE4 229 141 317 163 111 214 0.006049539 DOWN SQSTM1 1436 923 1949 1022 622 1421 0.00605211 DOWN PPP1R2 287 246 328 246 199 293 0.006082703 DOWN RAPGEF3 159 90 229 275 126 424 0.006089174 UP ARPC5 319 233 404 239 152 326 0.006090451 DOWN GTF2IRD2P 531 250 812 777 520 1035 0.006094246 UP LOC645452 752 411 1093 1188 638 1737 0.006107257 UP VPS24 229 145 312 168 119 217 0.006124901 DOWN XRCC5 218 169 267 166 105 228 0.006127431 DOWN DNAJC13 244 141 347 375 210 539 0.006159807 UP RPS11 2665 2543 2788 2294 1775 2814 0.006206458 DOWN CD151 169 126 211 129 95 163 0.006210633
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    seq2pathway Vignette Bin Wang, Xinan Holly Yang, Arjun Kinstlick May 19, 2021 Contents 1 Abstract 1 2 Package Installation 2 3 runseq2pathway 2 4 Two main functions 3 4.1 seq2gene . .3 4.1.1 seq2gene flowchart . .3 4.1.2 runseq2gene inputs/parameters . .5 4.1.3 runseq2gene outputs . .8 4.2 gene2pathway . 10 4.2.1 gene2pathway flowchart . 11 4.2.2 gene2pathway test inputs/parameters . 11 4.2.3 gene2pathway test outputs . 12 5 Examples 13 5.1 ChIP-seq data analysis . 13 5.1.1 Map ChIP-seq enriched peaks to genes using runseq2gene .................... 13 5.1.2 Discover enriched GO terms using gene2pathway_test with gene scores . 15 5.1.3 Discover enriched GO terms using Fisher's Exact test without gene scores . 17 5.1.4 Add description for genes . 20 5.2 RNA-seq data analysis . 20 6 R environment session 23 1 Abstract Seq2pathway is a novel computational tool to analyze functional gene-sets (including signaling pathways) using variable next-generation sequencing data[1]. Integral to this tool are the \seq2gene" and \gene2pathway" components in series that infer a quantitative pathway-level profile for each sample. The seq2gene function assigns phenotype-associated significance of genomic regions to gene-level scores, where the significance could be p-values of SNPs or point mutations, protein-binding affinity, or transcriptional expression level. The seq2gene function has the feasibility to assign non-exon regions to a range of neighboring genes besides the nearest one, thus facilitating the study of functional non-coding elements[2]. Then the gene2pathway summarizes gene-level measurements to pathway-level scores, comparing the quantity of significance for gene members within a pathway with those outside a pathway.
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus

    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.
  • Steroid-Dependent Regulation of the Oviduct: a Cross-Species Transcriptomal Analysis

    Steroid-Dependent Regulation of the Oviduct: a Cross-Species Transcriptomal Analysis

    University of Kentucky UKnowledge Theses and Dissertations--Animal and Food Sciences Animal and Food Sciences 2015 Steroid-dependent regulation of the oviduct: A cross-species transcriptomal analysis Katheryn L. Cerny University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Cerny, Katheryn L., "Steroid-dependent regulation of the oviduct: A cross-species transcriptomal analysis" (2015). Theses and Dissertations--Animal and Food Sciences. 49. https://uknowledge.uky.edu/animalsci_etds/49 This Doctoral Dissertation is brought to you for free and open access by the Animal and Food Sciences at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Animal and Food Sciences by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known.