Genome-Wide mRNA and lncRNA Expression Profiling to Uncover Their Role in the Molecular Pathogenesis of Developmental Dysplasia of the Hip
Abstract
1. Introduction
2. Results
2.1. Mapping Efficiency
2.2. Differentially Expressed Genes in Hip Joint Capsules of DDH Patients
2.3. Functional Enrichment Analysis of DEGs
2.4. Identification of Long Non-Coding RNAs
3. Discussion
4. Materials and Methods
4.1. Data Acquisition
4.2. Transcript Data Analysis
4.3. Functional Enrichment Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
DDH | Developmental dysplasia of the hip |
LncRNA | Long non-coding RNA |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
DEGs | Differentially expressed genes |
MF | Molecular function |
BP | Biological process |
CC | Cellular component |
MMP13 | Matrix Metalloproteinase 13 |
MMP3 | Matrix Metalloproteinase 3 |
GDF5 | Growth Differentiation Factor 5 |
DKK1 | Dickkopf WNT Signaling Pathway Inhibitor 1 |
WIF1 | Wnt Inhibitor Factor 1 |
MYOC | Myocilin |
IRX | Iroquois Homeobox |
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ID | Treatment | Mapping Rate (%) | Read Number (2 × 150 bp) |
---|---|---|---|
SRR14055716 | DDH | 80.74 | 24,847,026 |
SRR14055717 | DDH | 84.91 | 33,533,704 |
SRR14055718 | DDH | 80.85 | 23,836,127 |
SRR14055719 | DDH | 98.25 | 27,104,541 |
SRR14055720 | DDH | 87.71 | 24,866,901 |
SRR14055721 | DDH | 94.21 | 30,621,536 |
SRR14055722 | Control | 85.35 | 23,421,990 |
SRR14055723 | Control | 93.55 | 23,402,707 |
SRR14055724 | Control | 83.99 | 25,453,109 |
SRR14055725 | Control | 83.48 | 20,408,199 |
SRR14055726 | Control | 91.22 | 25,169,198 |
SRR14055727 | Control | 90.25 | 21,844,255 |
ID | log2 Fold Change | p-Value | Regulation in DDH |
---|---|---|---|
ENSG00000034971 | −9.1 | 1.82 × 10−33 | Up |
ENSG00000309097 | −7.6 | 0.011025698 | Up |
ENSG00000256513 | −7 | 2.82 × 10−6 | Up |
ENSG00000170549 | −6.5 | 7.46 × 10−9 | Up |
ENSG00000250421 | −6.5 | 2.88 × 10−7 | Up |
ENSG00000279096 | −6.4 | 1.67 × 10−5 | Up |
ENSG00000306524 | −6.2 | 5.87 × 10−8 | Up |
ENSG00000168447 | −5.9 | 1.51 × 10−14 | Up |
ENSG00000240654 | −5.6 | 4.60 × 10−7 | Up |
ENSG00000160097 | −5.5 | 3.54 × 10−9 | Up |
ENSG00000286415 | −5.4 | 0.000715357 | Up |
ENSG00000305982 | −5.4 | 0.007306598 | Up |
ENSG00000305491 | −5.4 | 0.010014926 | Up |
ENSG00000181408 | −5.3 | 2.18 × 10−9 | Up |
ENSG00000179915 | −5.3 | 6.20 × 10−9 | Up |
ENSG00000156076 | −5.3 | 1.73 × 10−5 | Up |
ENSG00000271239 | −5.3 | 0.015421818 | Up |
ENSG00000142973 | −5.2 | 7.44 × 10−12 | Up |
ENSG00000214866 | −5.2 | 2.19 × 10−5 | Up |
ENSG00000118733 | −5.2 | 0.000432547 | Up |
ENSG00000274833 | −5.2 | 0.002264803 | Up |
ENSG00000265962 | −5.2 | 0.004283014 | Up |
ENSG00000301580 | −5.1 | 5.39 × 10−6 | Up |
ENSG00000188803 | −5.1 | 2.66 × 10−5 | Up |
ENSG00000305239 | −5.1 | 0.000191428 | Up |
ENSG00000229236 | 6.5 | 1.94 × 10−6 | Down |
ENSG00000187689 | 6.5 | 4.20 × 10−6 | Down |
ENSG00000149968 | 6.6 | 1.96 × 10−14 | Down |
ENSG00000266604 | 6.7 | 1.93 × 10−5 | Down |
ENSG00000116147 | 6.7 | 0.002750078 | Down |
ENSG00000211934 | 6.7 | 0.025736049 | Down |
ENSG00000231131 | 6.8 | 9.52 × 10−11 | Down |
ENSG00000012817 | 6.8 | 2.32 × 10−6 | Down |
ENSG00000211660 | 6.8 | 0.023562957 | Down |
ENSG00000249306 | 6.9 | 9.30 × 10−17 | Down |
ENSG00000260197 | 6.9 | 1.98 × 10−7 | Down |
ENSG00000229876 | 7 | 1.05 × 10−6 | Down |
ENSG00000183878 | 7 | 4.61 × 10−6 | Down |
ENSG00000114374 | 7.1 | 4.07 × 10−7 | Down |
ENSG00000067048 | 7.2 | 2.85 × 10−14 | Down |
ENSG00000126545 | 7.2 | 5.33 × 10−9 | Down |
ENSG00000129824 | 7.3 | 3.60 × 10−8 | Down |
ENSG00000231535 | 7.4 | 2.40 × 10−8 | Down |
ENSG00000211598 | 7.5 | 4.07 × 10−7 | Down |
ENSG00000165246 | 7.5 | 1.11 × 10−6 | Down |
ENSG00000266995 | 7.7 | 6.79 × 10−14 | Down |
ENSG00000291033 | 7.7 | 7.11 × 10−14 | Down |
ENSG00000067646 | 7.9 | 1.88 × 10−13 | Down |
ENSG00000137745 | 8.7 | 5.16 × 10−26 | Down |
ENSG00000198692 | 9.4 | 8.86 × 10−7 | Down |
Cluster Number | Cluster Color | Gene Count | Primary Description |
---|---|---|---|
1 | Red | 339 | Immune response |
2 | Brown | 266 | Mitotic cell cycle process |
3 | Dark goldenrod | 255 | Extracellular matrix |
4 | Green-yellow | 133 | - |
5 | Green 2 | 65 | - |
6 | Green | 56 | - |
7 | Blue | 53 | - |
8 | Light sky blue | 41 | Postsynaptic cell membrane and protein–protein interactions at synapses |
9 | Medium blue | 25 | ncRNAs involved in Wnt signaling in hepatocellular carcinoma, and regulation of FZD by ubiquitination |
10 | Purple | 16 | O-linked glycosylation of mucins |
ID | BaseMean | Log2 Fold Change | lfcSE | Stat | p-Value | padj | Regulation in DDH |
---|---|---|---|---|---|---|---|
ENSG00000309097 | 20.0553182 | −7.6 | 3.00449956 | −2.5418833 | 0.0110257 | 0.12197728 | Up |
ENSG00000256513 | 12.8646141 | −7 | 1.49363454 | −4.6834569 | 2.82 × 10−6 | 0.00036368 | Up |
ENSG00000250421 | 13.1509542 | −6.5 | 1.2755177 | −5.1312126 | 2.88 × 10−7 | 6.37 × 10−5 | Up |
ENSG00000306524 | 7.35762862 | −6.2 | 1.14212948 | −5.4227401 | 5.87 × 10−8 | 1.76 × 10−5 | Up |
ENSG00000286415 | 4.37306511 | −5.4 | 1.6074669 | −3.3836247 | 0.00071536 | 0.02130454 | Up |
ENSG00000305982 | 4.31991575 | −5.4 | 2.0210034 | −2.6825374 | 0.0073066 | 0.09516642 | Up |
ENSG00000305491 | 4.18734128 | −5.4 | 2.08974346 | −2.5753135 | 0.01001493 | 0.1148278 | Up |
ENSG00000271239 | 12.0861402 | −5.3 | 2.17536921 | −2.4223187 | 0.01542182 | 0.1463899 | Up |
ENSG00000274833 | 3.70182773 | −5.2 | 1.70130402 | −3.0531135 | 0.0022648 | 0.04671496 | Up |
ENSG00000265962 | 3.6288218 | −5.2 | 1.81060089 | −2.8565286 | 0.00428301 | 0.07013193 | Up |
ENSG00000301580 | 6.83679945 | −5.1 | 1.11596197 | −4.5490905 | 5.39 × 10−6 | 0.00057765 | Up |
ENSG00000305239 | 6.90491206 | −5.1 | 1.36677843 | −3.7300681 | 0.00019143 | 0.00839207 | Up |
ENSG00000233845 | 3.34256322 | −5.1 | 1.40746917 | −3.5916966 | 0.00032853 | 0.01242405 | Up |
ENSG00000300502 | 3.29931021 | −5 | 1.71918577 | −2.9309225 | 0.00337957 | 0.06050065 | Up |
ENSG00000295404 | 12.0694117 | −5 | 2.17474927 | −2.2856073 | 0.02227725 | 0.18085266 | Up |
ENSG00000307068 | 4.26292628 | −4.9 | 1.76580602 | −2.7621872 | 0.00574155 | 0.08279327 | Up |
ENSG00000226562 | 2.83969294 | −4.8 | 2.15712697 | −2.2323878 | 0.02558934 | 0.19291473 | Up |
ENSG00000267653 | 18.6393025 | −4.6 | 1.18355532 | −3.8857992 | 0.00010199 | 0.00535485 | Up |
ENSG00000298690 | 2.40410301 | −4.6 | 1.31131045 | −3.4816176 | 0.0004984 | 0.01688615 | Up |
ENSG00000304163 | 3.60829109 | −4.6 | 1.63774551 | −2.8282687 | 0.00468005 | 0.07329761 | Up |
ENSG00000300437 | 2.48886314 | −4.6 | 1.7087183 | −2.7103252 | 0.00672173 | 0.09071955 | Up |
ENSG00000293757 | 2.45471648 | −4.6 | 2.2150069 | −2.0801695 | 0.03750999 | 0.23607729 | Up |
ENSG00000285649 | 2.24907601 | −4.5 | 1.49009445 | −3.006602 | 0.00264185 | NA | Up |
ENSG00000276831 | 2.26891435 | −4.5 | 2.15967333 | −2.084345 | 0.03712879 | NA | Up |
ENSG00000224239 | 3.14919595 | −4.4 | 1.21015928 | −3.6694311 | 0.00024309 | 0.00996896 | Up |
ENSG00000296719 | 2.07942702 | −4.4 | 1.29583942 | −3.3770964 | 0.00073255 | NA | Up |
ENSG00000295613 | 2.11341551 | −4.4 | 1.77626226 | −2.4722183 | 0.01342775 | NA | Up |
ENSG00000298074 | 43.2261772 | −4.3 | 0.68673232 | −6.227569 | 4.74 × 10−10 | 3.71 × 10−7 | Up |
ENSG00000274478 | 3.94265842 | −4.3 | 1.38362988 | −3.0753408 | 0.00210262 | 0.04461646 | Up |
ENSG00000227487 | 4.06682931 | −4.3 | 1.58140449 | −2.721663 | 0.00649543 | 0.08932244 | Up |
ENSG00000231132 | 1.92513856 | −4.3 | 1.86805998 | −2.2793749 | 0.02264479 | NA | Up |
ENSG00000296003 | 1.94909901 | −4.3 | 1.89990295 | −2.2485052 | 0.02454399 | NA | Up |
ENSG00000298193 | 1.92079493 | −4.3 | 1.96128058 | −2.16822 | 0.03014195 | NA | Up |
ENSG00000285936 | 1.97756865 | −4.3 | 2.1797068 | −1.9693765 | 0.04890988 | NA | Up |
ENSG00000300255 | 1.91034707 | −4.2 | 1.34504573 | −3.1580307 | 0.00158839 | NA | Up |
ENSG00000286468 | 1.92446954 | −4.2 | 1.69334955 | −2.5096469 | 0.0120852 | NA | Up |
ENSG00000297456 | 1.79753544 | −4.2 | 1.97057075 | −2.1102525 | 0.03483661 | NA | Up |
ENSG00000264007 | 2.74415058 | −4.2 | 2.02575856 | −2.0950347 | 0.0361679 | 0.23135695 | Up |
ENSG00000231419 | 10.5586343 | −4.1 | 0.95511704 | −4.2721184 | 1.94 × 10−5 | 0.00153673 | Up |
ENSG00000297199 | 9.18829618 | −4.1 | 1.06625967 | −3.8898188 | 0.00010032 | 0.00528289 | Up |
ENSG00000305011 | 2.48231308 | −4.1 | 1.18927314 | −3.4505029 | 0.00055954 | 0.01805428 | Up |
ENSG00000229495 | 1.74392169 | −4.1 | 1.5299145 | −2.6866744 | 0.00721673 | NA | Up |
ENSG00000275358 | 3.47818747 | −4.1 | 1.70141215 | −2.4009139 | 0.01635418 | 0.15200984 | Up |
ENSG00000300949 | 1.67487121 | −4.1 | 1.84983805 | −2.1963248 | 0.0280687 | NA | Up |
ENSG00000286411 | 2.505807 | −4.1 | 1.89232231 | −2.1742414 | 0.02968701 | 0.20751407 | Up |
ENSG00000285686 | 3.5641727 | −4.1 | 1.91437549 | −2.1534663 | 0.03128205 | 0.21402918 | Up |
ENSG00000286818 | 6.03882055 | −4 | 1.25554434 | −3.2155005 | 0.00130217 | 0.0325075 | Up |
ENSG00000294628 | 1.600431 | −4 | 1.54122597 | −2.5909005 | 0.00957252 | NA | Up |
ENSG00000300397 | 3.36778179 | −4 | 1.71935962 | −2.3439341 | 0.01908155 | 0.1658802 | Up |
ENSG00000234944 | 3.24048221 | −4 | 1.72676428 | −2.2928222 | 0.02185824 | 0.1789809 | Up |
ENSG00000204971 | 3.44993353 | 5.4 | 1.39793787 | 3.84619167 | 0.00011997 | 0.00603911 | Down |
ENSG00000298268 | 3.46510039 | 5.4 | 1.48640556 | 3.60463808 | 0.00031259 | 0.01198425 | Down |
ENSG00000258183 | 4.83347254 | 5.4 | 1.56660674 | 3.41522649 | 0.00063729 | 0.01970541 | Down |
ENSG00000303389 | 67.4491212 | 5.4 | 1.59960987 | 3.39016959 | 0.00069849 | 0.02101712 | Down |
ENSG00000249667 | 3.57232375 | 5.4 | 1.78879945 | 3.02570312 | 0.00248056 | 0.04947514 | Down |
ENSG00000249993 | 3.51827941 | 5.4 | 1.81714131 | 2.96381834 | 0.00303848 | 0.05650863 | Down |
ENSG00000310062 | 3.48578139 | 5.4 | 1.8301654 | 2.93439046 | 0.00334204 | 0.06010549 | Down |
ENSG00000304111 | 3.54345937 | 5.4 | 1.85545923 | 2.90663633 | 0.00365338 | 0.06364457 | Down |
ENSG00000308399 | 3.52372208 | 5.4 | 2.06650839 | 2.60844294 | 0.00909552 | 0.10839416 | Down |
ENSG00000290670 | 3.52399192 | 5.4 | 2.08902577 | 2.57982723 | 0.00988498 | 0.1137742 | Down |
ENSG00000300640 | 3.53914029 | 5.4 | 2.12685373 | 2.53647022 | 0.01119763 | 0.12259215 | Down |
ENSG00000306164 | 3.45792879 | 5.4 | 2.15200616 | 2.49173312 | 0.01271215 | 0.13155437 | Down |
ENSG00000250822 | 3.60090773 | 5.4 | 2.48073063 | 2.18592409 | 0.02882116 | 0.20492453 | Down |
ENSG00000290840 | 5.17888445 | 5.5 | 1.50803576 | 3.61858637 | 0.00029622 | 0.01151552 | Down |
ENSG00000300947 | 3.78576114 | 5.5 | 1.63901592 | 3.34744641 | 0.0008156 | 0.02356484 | Down |
ENSG00000289707 | 3.82574307 | 5.5 | 1.73352772 | 3.18330533 | 0.00145604 | 0.03503209 | Down |
ENSG00000300565 | 3.73979054 | 5.5 | 1.7681675 | 3.09858123 | 0.0019445 | 0.04225892 | Down |
ENSG00000250348 | 3.81618728 | 5.5 | 2.45002286 | 2.2518587 | 0.0243312 | 0.1891298 | Down |
ENSG00000230838 | 194.501423 | 5.6 | 0.70577156 | 7.98793817 | 1.37 × 10−15 | 3.81 × 10−12 | Down |
ENSG00000298768 | 22.8322869 | 5.6 | 0.95737791 | 5.85599323 | 4.74 × 10−9 | 2.68 × 10−6 | Down |
ENSG00000224099 | 4.19313483 | 5.6 | 1.77249083 | 3.18113846 | 0.00146698 | 0.03521975 | Down |
ENSG00000308513 | 5.8501961 | 5.6 | 1.88810388 | 2.97828392 | 0.00289867 | 0.05482292 | Down |
ENSG00000295056 | 4.32612076 | 5.7 | 1.36349558 | 4.18252197 | 2.88 × 10−5 | 0.00207142 | Down |
ENSG00000259937 | 8.83425397 | 5.7 | 1.44977142 | 3.95282857 | 7.72 × 10−5 | 0.00441933 | Down |
ENSG00000288015 | 4.27678936 | 5.7 | 1.46219699 | 3.87282695 | 0.00010758 | 0.00555274 | Down |
ENSG00000308731 | 4.33753956 | 5.7 | 1.55232652 | 3.66561513 | 0.00024675 | 0.01005271 | Down |
ENSG00000288049 | 4.24690662 | 5.7 | 1.69421782 | 3.34957101 | 0.00080937 | 0.02348628 | Down |
ENSG00000253554 | 4.33106158 | 5.7 | 1.7507366 | 3.24846626 | 0.00116029 | 0.03006132 | Down |
ENSG00000232596 | 6.40357577 | 5.8 | 1.51402082 | 3.79913474 | 0.0001452 | 0.00686811 | Down |
ENSG00000298049 | 4.64546188 | 5.8 | 1.77170343 | 3.26603666 | 0.00109064 | 0.02881119 | Down |
ENSG00000294222 | 17.6914436 | 5.9 | 1.47771016 | 4.01898815 | 5.84 × 10−5 | 0.00358626 | Down |
ENSG00000293442 | 155.369799 | 5.9 | 1.48639466 | 3.93570269 | 8.30 × 10−5 | 0.00466193 | Down |
ENSG00000264985 | 5.19724286 | 5.9 | 1.56786443 | 3.79214101 | 0.00014935 | 0.00698876 | Down |
ENSG00000294508 | 5.07296798 | 5.9 | 1.75683438 | 3.36730502 | 0.00075907 | 0.02236649 | Down |
ENSG00000251670 | 5.27532038 | 6 | 1.25670454 | 4.7454957 | 2.08 × 10−6 | 0.00029154 | Down |
ENSG00000233854 | 5.74368619 | 6.1 | 1.30938943 | 4.65113408 | 3.30 × 10−6 | 0.0004047 | Down |
ENSG00000286028 | 5.90442962 | 6.1 | 1.45659643 | 4.21037416 | 2.55 × 10−5 | 0.00189082 | Down |
ENSG00000298839 | 32.2989896 | 6.2 | 1.03885417 | 5.94096616 | 2.83 × 10−9 | 1.80 × 10−6 | Down |
ENSG00000293047 | 12.2817787 | 6.2 | 1.11489762 | 5.57238667 | 2.51 × 10−8 | 8.72 × 10−6 | Down |
ENSG00000249343 | 8.40798677 | 6.2 | 1.55287593 | 3.96157443 | 7.45 × 10−5 | 0.00429032 | Down |
ENSG00000176728 | 57.9891864 | 6.5 | 1.11309151 | 5.79756785 | 6.73 × 10−9 | 3.12 × 10−6 | Down |
ENSG00000271216 | 15.2594445 | 6.5 | 1.36837552 | 4.77529373 | 1.79 × 10−6 | 0.0002611 | Down |
ENSG00000229236 | 10.3349528 | 6.5 | 1.35769107 | 4.75996551 | 1.94 × 10−6 | 0.00027647 | Down |
ENSG00000266604 | 8.70411474 | 6.7 | 1.56681229 | 4.27280749 | 1.93 × 10−5 | 0.00153597 | Down |
ENSG00000231131 | 18.9261187 | 6.8 | 1.05759833 | 6.47436337 | 9.52 × 10−11 | 8.31 × 10−8 | Down |
ENSG00000249306 | 151.620051 | 6.9 | 0.82875406 | 8.3133538 | 9.30 × 10−17 | 4.06 × 10−13 | Down |
ENSG00000260197 | 19.7348345 | 6.9 | 1.32944921 | 5.20130859 | 1.98 × 10−7 | 4.72 × 10−5 | Down |
ENSG00000229876 | 10.5213785 | 7 | 1.42708418 | 4.88236894 | 1.05 × 10−6 | 0.00017407 | Down |
ENSG00000231535 | 27.0797506 | 7.4 | 1.32158065 | 5.58007893 | 2.40 × 10−8 | 8.44 × 10−6 | Down |
ENSG00000291033 | 276.125148 | 7.7 | 1.03227535 | 7.48581379 | 7.11 × 10−14 | 1.21 × 10−10 | Down |
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Kaya, İ.; Türktaş, M.; Yaş, S.; Bircan, R. Genome-Wide mRNA and lncRNA Expression Profiling to Uncover Their Role in the Molecular Pathogenesis of Developmental Dysplasia of the Hip. Int. J. Mol. Sci. 2025, 26, 8058. https://doi.org/10.3390/ijms26168058
Kaya İ, Türktaş M, Yaş S, Bircan R. Genome-Wide mRNA and lncRNA Expression Profiling to Uncover Their Role in the Molecular Pathogenesis of Developmental Dysplasia of the Hip. International Journal of Molecular Sciences. 2025; 26(16):8058. https://doi.org/10.3390/ijms26168058
Chicago/Turabian StyleKaya, İbrahim, Mine Türktaş, Semih Yaş, and Resul Bircan. 2025. "Genome-Wide mRNA and lncRNA Expression Profiling to Uncover Their Role in the Molecular Pathogenesis of Developmental Dysplasia of the Hip" International Journal of Molecular Sciences 26, no. 16: 8058. https://doi.org/10.3390/ijms26168058
APA StyleKaya, İ., Türktaş, M., Yaş, S., & Bircan, R. (2025). Genome-Wide mRNA and lncRNA Expression Profiling to Uncover Their Role in the Molecular Pathogenesis of Developmental Dysplasia of the Hip. International Journal of Molecular Sciences, 26(16), 8058. https://doi.org/10.3390/ijms26168058