Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statements
2.2. Sample Collection
2.3. RNA Sequencing
2.4. Data Processing
2.5. Differential Expression Analysis
2.6. IPA Analysis
2.7. Gene Ontology
3. Results
3.1. Read Alignments and Results
3.2. Differential Expression Analysis
3.2.1. Classification
3.2.2. Comparison of A vs. B
3.2.3. Group A
3.2.4. Group B
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Ingenuity Canonical Pathways | -log (p-Value) | z-Score | Molecules |
---|---|---|---|
Estrogen Receptor Signaling | 4.1 | 1.569 | ADCY1, ADCY5, ADCY9, CACNA1C, CARM1, CREB5, CREBBP, DDX5, FBXO32, FOXO4, GNAZ, GPS2, IGF2R, MAP2K2, MED4, MMP14, MMP15, MMP16, MMP2, NCOR2, NOS3, NOTCH1, PIK3CB, PLCB3, PRKACA, TRIM63 |
Endocannabinoid Cancer Inhibition Pathway | 3.89 | −1.807 | ADCY1, ADCY5, ADCY9, CREB5, CREBBP, DDIT3, MAP2K2, MAP2K7, MMP2, NOS1, NOS2, NOS3, NUPR1, PIK3CB, PRKACA |
Semaphorin Neuronal Repulsive Signaling Pathway | 3.48 | −0.535 | CSPG4, ITGA3, MAP2K2, MAP2K7, MAPT, PAK4, PDE4A, PIK3CB, PLXNA1, PLXNA2, PLXND1, PRKACA, SEMA3E, SMC3 |
GNRH Signaling | 3.47 | 1.941 | ADCY1, ADCY5, ADCY9, CACNA1C, CACNA1G, CACNA1H, CREB5, CREBBP, HBEGF, MAP2K2, MAP2K7, MAP3K11, MMP2, PAK4, PLCB3, PRKACA |
Corticotropin Releasing Hormone Signaling | 3.3 | 1.387 | ADCY1, ADCY5, ADCY9, CACNA1C, CACNA1G, CACNA1H, CREB5, CREBBP, MAP2K2, NOS1, NOS2, NOS3, PRKACA, SLC39A7 |
Gαs Signaling | 2.93 | 2.111 | ADCY1, ADCY5, ADCY9, ADD3, ADRB2, CREB5, CREBBP, MAP2K2, PRKACA, RAPGEF2, RYR1 |
Spliceosomal Cycle | 2.92 | −2.646 | DDX46, DHX15, MAGOH, PRPF18, RBM8A, SLU7, ZNF830 |
Adrenomedullin signaling pathway | 2.86 | 2.673 | ADCY1, ADCY5, ADCY9, KCNH2, KCNN3, MAP2K2, MAP2K7, MMP2, MYLK2, NOS3, PIK3CB, PLCB3, PRKACA, RAMP2, RXRA, SLC39A7 |
White Adipose Tissue Browning Pathway | 2.77 | 2.887 | ADCY1, ADCY5, ADCY9, CACNA1C, CACNA1G, CACNA1H, CREB5, CREBBP, LDHD, PPARA, PRKACA, RXRA |
Calcium Signaling | 2.66 | 1.897 | ATP2A2, CACNA1C, CACNA1G, CACNA1H, CHRNG, CREB5, CREBBP, MICU1, MYH14, MYH7, MYH8, PPP3CB, PRKACA, RCAN1, RYR1, TP63 |
Ingenuity Canonical Pathways | -log (p-Value) | z-Score | Molecules |
---|---|---|---|
A1 vs. A2 | |||
Glycolysis I | 14 | 1.897 | ALDOA, ALDOC, ENO3, GPI, PFKL, PFKM, PGAM2, PGK1, PKM, TPI1 |
Gluconeogenesis I | 7.11 | 1.633 | ALDOA, ALDOC, ENO3, GPI, PGAM2, PGK1 |
Calcium Signaling | 5.71 | 1 | ATP2A1, ATP2B2, CASQ2, CREB3L4, MYH1, MYH11, MYL1, MYL6B, TNNI2, TNNT3, TPM1 |
Actin Cytoskeleton Signaling | 5.47 | 1.667 | ACTN3, DIAPH3, EGF, FGF9, HRAS, LIMK1, MYH1, MYH11, MYL1, MYL6B, MYLPF |
Protein Kinase A Signaling | 4.96 | 1.265 | CREB3L4, MYL1, MYL6B, MYLPF, NAPEPLD, PGP, PHKB, PLCL1, PLCL2, PPP1R3D, PTPN3, PYGM, TNNI2, UBASH3B |
Estrogen Receptor Signaling | 3.84 | 1.508 | BCL2, CREB3L4, EGF, HRAS, LIMK1, MYL1, MYL6B, MYLPF, PLCL1, PLCL2, SETD7 |
Apelin Cardiomyocyte Signaling Pathway | 3.65 | 1.633 | ATP2A1, MYL1, MYL6B, MYLPF, PLCL1, PLCL2 |
Synaptic Long Term Potentiation | 3.03 | 0.816 | CREB3L4, HRAS, PLCL1, PLCL2, PPP1R1A, PPP1R3D |
Semaphorin Neuronal Repulsive Signaling Pathway | 3.02 | 0.816 | DPYSL2, LIMK1, MYL1, MYL6B, MYLPF, VCAN |
PAK Signaling | 2.8 | 1.342 | HRAS, LIMK1, MYL1, MYL6B, MYLPF |
A1 vs. A3 | |||
iCOS-iCOSL Signaling in T Helper Cells | 24.8 | −4.359 | CAMK4, CD247,CD28, CD3D, CD3E, CD3G, CD4, CD80, CD86, FCER1G, HLA-DOA, HLA-DOB, HLA-DRA, ICOS, IKBKE, IL2RA, IL2RB, IL2RG, ITK, LAT, LCK, LCP2, PIK3CG, PTPRC, VAV1, ZAP70 |
CD28 Signaling in T Helper Cells | 23.8 | −3.771 | ARPC1B, CAMK4, CARD11, CD247, CD28, CD3D, CD3E, CD3G, CD4, CD80, CD86, FCER1G, HLA-DOA, HLA-DOB, HLA-DRA, IKBKE, ITK, LAT, LCK, LCP2, PIK3CG, PTPN6, PTPRC, SYK, VAV1, ZAP70 |
Th2 Pathway | 19.8 | −3.638 | CCR1, CD247, CD28, CD3D, CD3E, CD3G, CD4, CD80, CD86, CXCR4, HLA-DOA, HLA-DOB, HLA DRA, ICOS, IKZF1, IL2RA, IL2RB, IL2RG, ITGB2, JAK3, PIK3CG, SPI1, TIMD4, VAV1 |
Th1 Pathway | 17.2 | −3.638 | CD247, CD28, CD3D, CD3E, CD3G, CD4, CD80, CD86, CD8A, CXCR3, HLA-DOA, HLA-DOB, HLA-DRA, ICOS, IL10RA, IL18R1, IRF1, ITGB2, JAK3, PIK3CG, VAV1 |
PKCθ Signaling in T Lymphocytes | 16.1 | −4.69 | CARD11, CD247, CD28, CD3D, CD3E, CD3G, CD4, CD80, CD86, FCER1G, HLA-DOA, HLA-DOB, HLA-DRA, IKBKE, LAT, LCK, LCP2, PIK3CG, RAC2, VAV1, VAV3, ZAP70 |
Role of NFAT in Regulation of the Immune Response | 15.7 | −4.796 | CAMK4, CD247, CD28, CD3D, CD3E, CD3G, CD4, CD80, CD86, FCER1G, FCGR2C, HLA-DOA, HLA-DOB, HLA-DRA, IKBKE, ITK, LAT, LCK, LCP2, PIK3CG, PLCB2, SYK, ZAP70 |
Calcium-induced T Lymphocyte Apoptosis | 12.9 | −3.606 | ATP2A3, CAMK4, CD247, CD3D, CD3E, CD3G, CD4, FCER1G, HLA-DOA, HLA-DOB, HLA-DRA, LCK, PRKCB, ZAP70 |
PD-1, PD-L1 cancer immunotherapy pathway | 11.1 | 3.873 | CD247, CD28, CD80, HLA-DOA, HLA-DOB, HLA-DRA, IL2RA, IL2RB, IL2RG, JAK3, LAT, LCK, LCP2, PIK3CG, ZAP70 |
Type I Diabetes Mellitus Signaling | 10.8 | −2.828 | CASP8, CD247, CD28, CD3D, CD3E, CD3G, CD80, CD86, FCER1G, HLA-DOA, HLA-DOB, HLA-DRA, IKBKE, IRF1, PRF1 |
B Cell Receptor Signaling | 10.4 | −3.051 | APBB1IP, CAMK4, DAPP1, FCGR2C, IGHE, IGHG4, IGHM, IKBKE, PIK3AP1, PIK3CG, PRKCB, PTK2B, PTPN6, PTPRC, RAC2, SYK, VAV1, VAV3 |
A2 vs. A3 | |||
iCOS-iCOSL Signaling in T Helper Cells | 12.3 | −3.464 | CD3D, CD3E, CD4, FCER1G, HLA-DOA, ICOS, IL2RA, IL2RG, ITK, LCK, LCP2, PIK3CD, PIK3CG, PTPRC, VAV1, ZAP70 |
B Cell Receptor Signaling | 10.8 | −2.496 | CD22, CREB3L4, DAPP1, FCGR2C, IGHE, IGHG4, IGHM, MAP2K6, PIK3AP1, PIK3CD, PIK3CG, PLCG2, PRKCB, PTPRC, RAC2, RASSF5, SYNJ2, VAV1 |
Phospholipase C Signaling | 10.1 | −2.138 | CD3D, CD3E, CREB3L4, FCER1G, FCGR2C, IGHG4, ITGA4, ITK, LCK, LCP2, MYL2, MYL6B, MYLPF, NAPEPLD, PLCB2, PLCG2, PLD4, PRKCB, RAC2, ZAP70 |
Glycolysis I | 9.21 | −1.414 | ALDOA, ALDOC, ENO3, PFKL, PFKM, PGAM2, PGK1, PKM |
Actin Cytoskeleton Signaling | 8.71 | −1.604 | EGF, FGD3, FGF9, ITGA4, LIMK1, MYH1, MYH10, MYL2, MYL6B, MYLPF, NCKAP1L, PIK3CD, PIK3CG, RAC2, TIAM2, TMSB4Y, VAV1 |
CD28 Signaling in T Helper Cells | 8.51 | −3 | CD3D, CD3E, CD4, FCER1G, HLA-DOA, ITK, LCK, LCP2, PIK3CD, PIK3CG, PTPRC, VAV1, ZAP70 |
Calcium-induced T Lymphocyte Apoptosis | 8.11 | −3 | ATP2A1, ATP2A3, CD3D, CD3E, CD4, FCER1G, HLA-DOA, LCK, PRKCB, ZAP70 |
Ingenuity Canonical Pathways | -log (p-Value) | z-Score | Molecules |
---|---|---|---|
B1 vs. B2 | |||
Actin Cytoskeleton Signaling | 6.57 | 0.632 | ACTN3, ARHGAP24, EGF, FGF1, FGF10, FGF7, FGF9, HRAS, MYH1, MYH10, MYH3, MYL6B, MYLPF, PAK1, PFN2, TIAM2 |
Glycolysis I | 5.67 | 2.449 | ALDOA, ENO3, GPI, PGAM2, PGK1, PKM |
Oxidative Phosphorylation | 5.17 | 3.162 | COX4I1, COX5A, COX7A1, CYB5A, MT-ND4L, NDUFA8, NDUFS7, NDUFS8, NDUFV1, UQCR11 |
Gluconeogenesis I | 4.39 | 2.236 | ALDOA, ENO3, GPI, PGAM2, PGK1 |
Sirtuin Signaling Pathway | 3.78 | −1.732 | ARG2, IDH2, LDHA, MT-ND4L, NDUFA8, NDUFS7, NDUFS8, NDUFV1, PFKFB3, PGAM2, PGK1, PPIF, SREBF1, TUBA8 |
Calcium Signaling | 3.46 | −1 | CAMKK2, CASQ2, CREB3L4, MYH1, MYH10, MYH3, MYL6B, SLC8A3, TNNI2, TNNT3, TPM1 |
FGF Signaling | 2.74 | −0.816 | CREB3L4, FGF1, FGF10, FGF7, FGF9, HRAS |
Neuregulin Signaling | 2.45 | 0.447 | BTC, EGF, ERBIN, HRAS, RNF41, STAT5A |
Bladder Cancer Signaling | 2.43 | −0.447 | EGF, FGF1, FGF10, FGF7, FGF9, HRAS |
LPS/IL-1 Mediated Inhibition of RXR Function | 1.66 | 0.0357 | ABCB9, ACOX3, APOE, FABP4, MAOB, PLTP, SREBF1, TNFRSF11B |
B1 vs. B3 | |||
AMPK Signaling | 3.34 | 0.816 | ACACB, ADIPOQ, EIF4EBP1, PCK2, PFKFB3, PIK3R6, TBC1D1 |
Senescence Pathway | 2.07 | 1.633 | ACVR1C, DHCR24, E2F8, EIF4EBP1, PIK3R6, TGFB3 |
Synaptogenesis Signaling Pathway | 1.82 | 1.633 | APOE, CDH15, EIF4EBP1, GSK3B, PIK3R6, SNCG |
Factors Promoting Cardiogenesis in Vertebrates | 1.8 | 2 | ACVR1C, BMPR1B, GSK3B, TGFB3 |
Colorectal Cancer Metastasis Signaling | 1.63 | 2 | BAX, GSK3B, PIK3R6, PTGER3, TGFB3 |
Adrenomedullin signaling pathway | 1.42 | 1 | BAX, GSK3B, GUCY2C, PIK3R6 |
B2 vs. B3 | |||
Glycolysis I | 11.6 | −2.121 | ALDOA, ALDOC, ENO3, GPI, PFKM, PGAM2, PGK1, PKM |
Calcium Signaling | 8.23 | −0.447 | ATP2A1, CAMKK2, CASQ2, CREB3L4, MYH1, MYH3, MYL2, MYL6B, PPP3CA, TNNI2, TNNT3, TPM3 |
Gluconeogenesis I | 7.99 | −1.633 | ALDOA, ALDOC, ENO3, GPI, PGAM2, PGK1 |
Semaphorin Neuronal Repulsive Signaling Pathway | 4.79 | −0.378 | DPYSL2, DPYSL3, MYL2, MYL6B, PAK1, PDE4D, PLXNA3 |
Actin Cytoskeleton Signaling | 4.2 | −1.134 | ACTN3, EGF, MYH1, MYH3, MYL2, MYL6B, PAK1, SSH2 |
PFKFB4 Signaling Pathway | 3.74 | 1 | CREB3L4, GPI, PFK M, TGFB3 |
HIF1α Signaling | 2.76 | −1.633 | ADM, EGF, GPI, LDHA, PKM, PPP3CA |
Colanic Acid Building Blocks Biosynthesis | 2.49 | #NUM! | GPI, UGP2 |
White Adipose Tissue Browning Pathway | 2.08 | 1 | CAMKK2, CREB3L4, FNDC5, LDHA |
AMPK Signaling | 1.97 | 1 | CAMKK2, CREB3L4, GYS1, PFKM, ULK1 |
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Lee, H.-Y.; Kim, J.-Y.; Kim, K.H.; Jeong, S.; Cho, Y.; Kim, N. Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle. Genes 2020, 11, 1359. https://doi.org/10.3390/genes11111359
Lee H-Y, Kim J-Y, Kim KH, Jeong S, Cho Y, Kim N. Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle. Genes. 2020; 11(11):1359. https://doi.org/10.3390/genes11111359
Chicago/Turabian StyleLee, Ho-Yeon, Jae-Yoon Kim, Kyoung Hyoun Kim, Seongmun Jeong, Youngbum Cho, and Namshin Kim. 2020. "Gene Expression Profile in Similar Tissues Using Transcriptome Sequencing Data of Whole-Body Horse Skeletal Muscle" Genes 11, no. 11: 1359. https://doi.org/10.3390/genes11111359