Representative Tissue - Transcripts of Protein-coding Genes

There are many transcripts of human protein-coding genes identified through massive NGS sequence datasets. Alternative transcripts would provide diversified molecular functions in biological processes during development and evolution. It is essential for biomedical researchers to further interrogate the expression profiles of various transcripts in different tissues. In this study, we have utilized the GTEx dataset to thoroughly investigate the expression patterns of dominantly expressed transcripts in more than fifty normal human tissue types. Identification of tissue representative transcripts would be beneficial for understanding the biological functions of protein-coding genes in particular tissues. Herein, we designed the RTTPG database to list the tissue representative highly expressed transcripts of human protein-coding genes with particularly easy-to-use visualization interfaces. We previously reported that most of the human protein-coding genes maintain few dominant transcripts in terms of expression modulation. Thus, we provided the visualized tissue expression profiles of the top-ranked transcripts as well as defined preferential tissue expressed transcripts by the Z-score values. In the beginning tissue distribution graph below: Tissue specific representative transcripts of human protein-coding genes were noted by their Rank1 transcripts with the Z-score above three. Selecting the tissue subtypes will display the numbers of tissue representative gene transcripts.


Z-score ≥ 3; Rank1




Select Ranked Transcripts :  





This RTTPG web visualization tool is to offer distinct tissue expression profiles of dominant transcripts in human protein-coding genes. In previous studies, it is demonstrated that only few transcript isoforms are dominantly expressed among all the alternative transcript isoforms. In most cases, the top five transcript isoforms (Rank1 ~ Rank5) could occupy more than 90% of protein-coding gene expression levels. In the RTTPG database, we further provide options to interrogate the tissue expression information on the various top-ranked transcript isoforms (Rank1, Rank1~3; Rank1~5; Rank1~10 and all expressed transcripts). Users can choose the range of Top-ranked transcripts for their study needs. The numbers of Z-score ≥ 3 transcript isoforms in each tissue are listed in the following table.



Tissue Subtype Rank1 Rank ≤ 3 Rank ≤ 5 Rank ≤ 10 ALL
Adipose_Subcutaneous 180 478 678 947 1147
Adipose_Visceral (Omentum) 152 370 526 743 903
Adrenal Gland 346 829 1144 1622 1999
Artery_Aorta 293 783 1161 1695 2174
Artery_Coronary 67 157 212 278 347
Artery_Tibial 260 686 1041 1705 2370
Bladder 107 267 425 713 1103
Brain_Amygdala 28 71 100 144 218
Brain_Anterior cingulate cortex (BA24) 41 105 152 232 340
Brain_Caudate (basal ganglia) 97 212 272 365 449
Brain_Cerebellar Hemisphere 1561 4324 6555 10031 13112
Brain_Cerebellum 1237 3825 6027 9635 12859
Brain_Cortex 203 424 569 785 1002
Brain_Frontal Cortex (BA9) 471 1020 1362 1883 2463
Brain_Hippocampus 31 79 114 167 231
Brain_Hypothalamus 159 308 383 485 589
Brain_Nucleus accumbens (basal ganglia) 157 363 475 686 869
Brain_Putamen (basal ganglia) 46 108 140 186 238
Brain_Spinal cord (cervical c-1) 393 947 1369 2000 2672
Brain_Substantia nigra 48 119 149 212 290
Breast_Mammary Tissue 84 226 314 407 489
Cells_Cultured fibroblasts 1097 3314 5177 8152 10559
Cells_EBV-transformed lymphocytes 1658 4450 6764 10402 13219
Cervix_Ectocervix 152 440 792 1659 2714
Cervix_Endocervix 155 410 670 1329 2215
Colon_Sigmoid 116 288 365 516 657
Colon_Transverse 197 430 576 795 923
Esophagus_Gastroesophageal Junction 42 99 134 203 253
Esophagus_Mucosa 463 1089 1520 2094 2499
Esophagus_Muscularis 87 205 268 383 474
Fallopian Tube 300 796 1226 2141 3214
Heart_Atrial Appendage 129 319 460 687 887
Heart_Left Ventricle 129 338 471 653 824
Kidney_Cortex 197 496 692 966 1135
Kidney_Medulla 230 741 1114 1731 2423
Liver 588 1535 2141 2867 3333
Lung 343 1054 1653 2552 3115
Minor Salivary Gland 188 472 692 1008 1276
Muscle_Skeletal 573 1416 2008 2938 3832
Nerve_Tibial 372 1054 1690 2671 3375
Ovary 271 778 1193 1803 2308
Pancreas 141 349 506 671 792
Pituitary 535 1544 2287 3392 4178
Prostate 161 445 647 899 1068
Skin_Not Sun Exposed (Suprapubic) 555 1254 1759 2411 2898
Skin_Sun Exposed (Lower leg) 483 1113 1576 2205 2713
Small Intestine_Terminal Ileum 329 818 1174 1652 1973
Spleen 669 1999 2971 4197 4925
Stomach 97 221 301 422 487
Testis 3529 9457 14188 21692 27797
Thyroid 402 1162 1719 2548 3168
Uterus 128 349 521 775 1044
Vagina 80 243 378 543 667
Whole Blood 527 1263 1856 2747 3484
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