Long Non-Coding RNAs Target Pathogenetically Relevant Genes and Pathways in Rheumatoid Arthritis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patients
2.2. Microarray Analysis
2.3. Protein‒Protein Interaction (PPI) Network Construction and Network Clustering
2.4. Gene Functional Classification and Enrichment Analysis
2.5. Real-Time PCR of LncRNA
2.6. Real-Time PCR of Genes Modulated in RA Patients
2.7. Real-Time PCR of MicroRNA
2.8. Statistical Analysis
3. Results
3.1. High-Throughput Gene and Long Non-Coding RNA Expression Profiling in Peripheral Blood Mononuclear Cells of RA Patients
3.2. Selected Long Non-Coding RNAs Modulated in RA Patients Have the Potential to Regulate Genes Differentially Expressed in the Disease
3.3. LncRNA RP11-498C9.15 Targets RA-Associated Meaningful Signalling Pathways
3.4. LncRNA RP11-498C9.15 Targets Highly Connected Genes in the RA Transcriptome
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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ID | Fold Change | FDR p-Value | Gene Symbol | Description | mRNA Accession |
---|---|---|---|---|---|
Apoptosis | |||||
TC0300009843.hg.1 | 2.12 | 0.050 | TP63 | tumour protein p63 | NM_001114978 |
TC2200007783.hg.1 | 5.34 | 0.008 | PIM3 | Pim-3 proto-oncogene, serine/threonine kinase | NM_001001852 |
TC0300010770.hg.1 | 12.5 | 0.008 | CSRNP1 | cysteine-serine-rich nuclear protein 1 | NM_033027 |
TC1900009429.hg.1 | 2.3 | 0.018 | KHSRP | KH-type splicing regulatory protein | NM_003685 |
TC0600011441.hg.1 | 3.47 | 0.008 | BAG6 | BCL2-associated athanogene 6 | NM_001199697 |
TC1100013230.hg.1 | 2.08 | 0.023 | BCL9L | B-cell CLL/lymphoma 9-like | NM_182557 |
TC0100007449.hg.1 | 2.2 | 0.049 | SH3BGRL3 | SH3 domain binding glutamate-rich protein like 3 | NM_031286 |
TC1100006815.hg.1 | 3 | 0.037 | WEE1 | WEE1 G2 checkpoint kinase | NM_001143976 |
Cell proliferation | |||||
TC0300009702.hg.1 | 2.49 | 0.044 | EIF4G1 | eukaryotic translation initiation factor 4 gamma, 1 | NM_001194946 |
TC0X00007132.hg.1 | 3.18 | 0.008 | CDK16 | cyclin-dependent kinase 16 | NM_001170460 |
TC0200015764.hg.1 | 3.79 | 0.004 | CNPPD1 | cyclin Pas1/PHO80 domain containing 1 | NM_015680 |
TC0200016494.hg.1 | 2.04 | 0.046 | CNNM4 | cyclin and CBS domain divalent metal cation transport mediator 4 | NM_020184 |
TC1900010696.hg.1 | 5.13 | 0.007 | AKT2 | v-akt murine thymoma viral oncogene homolog 2 | NM_001243027 |
Cell migration | |||||
TC1500010018.hg.1 | 2.3 | 0.018 | SEMA7A | semaphorin 7A, GPI membrane anchor | NM_001146029 |
TC1200012859.hg.1 | 3.65 | 0.006 | RHOF | ras homolog family member F (in filopodia) | NM_019034 |
TC1100009864.hg.1 | 3.29 | 0.004 | RHOG | ras homolog family member G | NM_001665 |
TC1700009528.hg.1 | 2.46 | 0.028 | CXCL16 | chemokine (C-X-C motif) ligand 16 | NM_001100812 |
Inflammatory response | |||||
TC1500006925.hg.1 | 24.36 | 0.018 | THBS1 | thrombospondin 1 | NM_003246 |
TC1900006977.hg.1 | 11.9 | 0.050 | ICAM1 | intercellular adhesion molecule 1 | NM_000201 |
TC0500007231.hg.1 | 3.28 | 0.022 | PTGER4 | prostaglandin E receptor 4 (subtype EP4) | NM_000958 |
TC0100011384.hg.1 | 2.52 | 0.025 | MAPKAPK2 | mitogen-activated protein kinase-activated protein kinase 2 | NM_004759 |
TC0100009364.hg.1 | 3.82 | 0.008 | CSF1 | colony stimulating factor 1 (macrophage) | NM_000757 |
TC0300006985.hg.1 | 6.3 | 0.034 | CCR4 | chemokine (C-C motif) receptor 4 | NM_005508 |
TC1900010743.hg.1 | 2.7 | 0.019 | TGFB1 | transforming growth factor beta 1 | NM_000660 |
TC1000007990.hg.1 | 4.92 | 0.020 | DDIT4 | DNA damage inducible transcript 4 | NM_019058 |
TC1600011060.hg.1 | 2.28 | 0.017 | COTL1 | coactosin-like F-actin binding protein 1 | NM_021149 |
TC2000009401.hg.1 | 3.54 | 0.011 | SPATA2 | Spermatogenesis-associated 2 | NM_00113577 |
TC1100011243.hg.1 | 4.25 | 0.007 | RELA | v-rel avian reticuloendotheliosis viral oncogene homolog A | NM_001145138 |
TC0900011623.hg.1 | 2.16 | 0.030 | PTGES2 | prostaglandin E synthase 2 | NM_001256335 |
TC0200014672.hg.1 | 7.65 | 0.042 | NR4A2 | nuclear receptor subfamily 4, group A, member 2 | NM_006186 |
TC1900007270.hg.1 | 6.2 | 0.007 | KLF2 | Kruppel-like factor 2 | NM_016270 |
TC1700011903.hg.1 | 4.41 | 0.046 | SOCS3 | suppressor of cytokine signalling 3 | NM_003955 |
TC1600009395.hg.1 | 3.76 | 0.010 | SOCS1 | suppressor of cytokine signalling 1 | NM_003745 |
TC0100017107.hg.1 | 2.71 | 0.041 | IL10 | interleukin 10 | NM_000572 |
TC1100009225.hg.1 | 7.04 | 0.006 | CXCR5 | chemokine (C-X-C motif) receptor 5 | NM_001716 |
TC1100013178.hg.1 | 2.22 | 0.023 | MAP4K2 | mitogen-activated protein kinase kinase kinase kinase 2 | NM_001307990 |
TC1700007262.hg.1 | 4.43 | 0.023 | MAP2K3 | mitogen-activated protein kinase kinase 3 | NM_002756 |
TC1900009325.hg.1 | 3.56 | 0.038 | MAP2K2 | mitogen-activated protein kinase kinase 2 | NM_030662 |
TC0600011438.hg.1 | 2.07 | 0.045 | LTB | lymphotoxin beta (TNF superfamily, member 3) | NM_002341 |
TC1700011903.hg.1 | 4.41 | 0.046 | SOCS3 | suppressor of cytokine signalling 3 | NM_003955 |
Immune response | |||||
TC0200008452.hg.1 | 2.85 | 0.024 | MAL | mal, T-cell differentiation protein | NM_002371 |
TC1100006576.hg.1 | 3.74 | 0.015 | CD81 | CD81 molecule | NM_001297649 |
TC0600007495.hg.1 | 2.08 | 0.037 | HLA-A | major histocompatibility complex, class I, A | NM_001242758 |
TC0100007291.hg.1 | 2.08 | 0.028 | C1QC | complement component 1, q subcomponent, C chain | NM_001114101 |
TC1100007787.hg.1 | 3.29 | 0.035 | CD6 | CD6 molecule | NM_001254750 |
TC1600011368.hg.1 | 3.14 | 0.008 | LAT | linker for activation of T-cells | NM_001014987 |
TC1900008279.hg.1 | 5.58 | 0.006 | BCL3 | B-cell CLL/lymphoma 3 | NM_005178 |
TC1900008166.hg.1 | 3.13 | 0.004 | CD79A | CD79a molecule, immunoglobulin-associated alpha | NM_001783 |
TC1200010950.hg.1 | 2.47 | 0.034 | STAT6 | signal transducer and activator of transcription 6, interleukin-4 induced | NM_001178078 |
TC1000008891.hg.1 | 10.97 | 0.008 | DUSP5 | dual specificity phosphatase 5 | NM_004419 |
TC0600008972.hg.1 | 5.51 | 0.018 | PRDM1 | PR domain containing 1, with ZNF domain | NM_001198 |
TC0100016000.hg.1 | 4.15 | 0.004 | MEF2D | myocyte enhancer factor 2D | NM_001271629 |
TC0900008891.hg.1 | 2.21 | 0.023 | LRRC8A | leucine rich repeat containing 8 family, member A | NM_001127244 |
TC1900009320.hg.1 | 2.71 | 0.045 | ZBTB7A | zinc finger and BTB domain containing 7A | NM_015898 |
TC1900008505.hg.1 | 2.93 | 0.018 | BAX | BCL2-associated X protein | NM_001291428 |
TC1800007805.hg.1 | 2.22 | 0.027 | NFATC1 | nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1 | NM_001278669 |
TC2200008637.hg.1 | 3.64 | 0.015 | IL2RB | interleukin 2 receptor, beta | NM_000878 |
Angiogenesis | |||||
TC1200010839.hg.1 | 2 | 0.029 | ITGA5 | integrin alpha 5 | NM_002205 |
TC2000007336.hg.1 | 2.83 | 0.015 | PPP1R16B | protein phosphatase 1, regulatory subunit 16B | NM_001172735 |
TC1600008971.hg.1 | 2.83 | 0.018 | JMJD8 | jumonji domain containing 8 | NM_001005920 |
TC1700011818.hg.1 | 2.6 | 0.050 | JMJD6 | jumonji domain containing 6 | NM_001081461 |
TC0100007832.hg.1 | 17.12 | 0.008 | ZC3H12A | zinc finger CCCH-type containing 12A | NM_025079 |
TC0100018300.hg.1 | 2.44 | 0.032 | ADAM15 | ADAM metallopeptidase domain 15 | NM_001261464 |
Bone resorption | |||||
Positive regulation of bone resorption | |||||
TC0X00008831.hg.1 | 2.62 | 0.021 | ATP6AP1 | ATPase, H+ transporting, lysosomal accessory protein 1 | NM_001183 |
TC2000007283.hg.1 | 2.11 | 0.026 | SRC | SRC proto-oncogene, non-receptor tyrosine kinase | NM_005417 |
TC0300009916.hg.1 | 4.17 | 0.030 | HES1 | hes family bHLH transcription factor 1 | NM_005524 |
TC0100015891.hg.1 | 2.76 | 0.008 | CRTC2 | CREB regulated transcription coactivator 2 | NM_181715 |
TC1900010009.hg.1 | 3.41 | 0.023 | JUND | jun D proto-oncogene | NM_001286968 |
Positive regulation of osteoclast proliferation/differentiation | |||||
TC0300007380.hg.1 | 2.4 | 0.027 | TCTA | T-cell leukaemia translocation altered | NM_022171 |
TC1900009134.hg.1 | 9.56 | 0.002 | SBNO2 | strawberry notch homolog 2 | NM_014963 |
TC0100009364.hg.1 | 3.82 | 0.008 | CSF1 | colony stimulating factor 1 (macrophage) | NM_000757 |
TC0X00008831.hg.1 | 2.62 | 0.021 | ATP6AP1 | ATPase, H+ transporting, lysosomal accessory protein 1 | NM_001183 |
TC0300009916.hg.1 | 4.17 | 0.030 | HES1 | hes family bHLH transcription factor 1 | NM_005524 |
TC0500007231.hg.1 | 3.28 | 0.022 | PTGER4 | prostaglandin E receptor 4 (subtype EP4) | NM_000958 |
TC1900007096.hg.1 | 5.16 | 0.032 | JUNB | jun B proto-oncogene | NM_002229 |
Osteoblast differentiation | |||||
TC2000009887.hg.1 | −2.8 | 0.0172 | PLCB1 | phospholipase C, beta 1 (phosphoinositide-specific) | NM_015192 |
Extracellular matrix degradation | |||||
TC2000007514.hg.1 | 3.14 | 0.041 | MMP9 | matrix metallopeptidase 9 | NM_004994 |
TC0500012599.hg.1 | 1.9 | 0.040 | ADAM19 | ADAM metallopeptidase domain 19 | NM_033274 |
TC0100018300.hg.1 | 2.44 | 0.032 | ADAM15 | ADAM metallopeptidase domain 15 | NM_001261464 |
TC1900006470.hg.1 | 3.01 | 0.011 | BSG | basigin | NM_001728 |
ID | Fold Change | FDR p-Value | Gene Symbol | Description | mRNA Accession |
---|---|---|---|---|---|
Wnt signalling pathway | |||||
TC1900009272.hg.1 | 2.4 | 0.018 | AES | amino-terminal enhancer of split | NM_001130 |
TC1100008181.hg.1 | 2.03 | 0.029 | LRP5 | LDL-receptor-related protein 5 | NM_001291902 |
TC0200014672.hg.1 | 7.65 | 0.042 | NR4A2 | nuclear receptor subfamily 4, group A, member 2 | NM_006186 |
TC1100007913.hg.1 | 2.69 | 0.048 | MARK2 | MAP/microtubule affinity-regulating kinase 2 | NM_001039469 |
TC1200007595.hg.1 | 2.88 | 0.023 | SMARCD1 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 1 | NM_003076 |
TC1900011639.hg.1 | 2.1 | 0.032 | STK11 | serine/threonine kinase 11 | NM_000455 |
TC1100008181.hg.1 | 2.03 | 0.029 | LRP5 | LDL-receptor-related protein 5 | NM_001291902 |
TNF signalling pathway | |||||
TC0900011385.hg.1 | −1.99 | 0.040 | PSMD5 | proteasome 26S subunit, non-ATPase 5 | NM_001270427 |
TC0600011438.hg.1 | 2.07 | 0.045 | LTB | lymphotoxin beta (TNF superfamily, member 3) | NM_002341 |
TC1700010879.hg.1 | 2.36 | 0.026 | MAP3K14 | mitogen-activated protein kinase kinase kinase 14 | NM_003954 |
TC1600010616.hg.1 | 2.14 | 0.035 | TRADD | TNFRSF1A-associated via death domain | NM_003789 |
TC1100011243.hg.1 | 4.25 | 0.007 | RELA | v-rel avian reticuloendotheliosis viral oncogene homolog A | NM_001145138 |
Type I interferon signalling | |||||
TC0600007495.hg.1 | 2.08 | 0.037 | HLA-A | major histocompatibility complex, class I, A | NM_001242758 |
TC0200008452.hg.1 | 2.85 | 0.024 | MAL | mal, T-cell differentiation protein | NM_002371 |
TC0100017107.hg.1 | 2.71 | 0.041 | IL10 | interleukin 10 | NM_000572 |
TC1600009395.hg.1 | 3.76 | 0.010 | SOCS1 | suppressor of cytokine signalling 1 | NM_003745 |
TC1100011243.hg.1 | 4.25 | 0.007 | RELA | v-rel avian reticuloendotheliosis viral oncogene homolog A | NM_001145138 |
TC1900009627.hg.1 | 2.63 | 0.040 | TYK2 | tyrosine kinase 2 | NM_003331 |
TC1000008727.hg.1 | 2.64 | 0.024 | NFKB2 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100) | NM_001077494 |
p38 MAP kinase signalling | |||||
TC1400009524.hg.1 | 2.91 | 0.029 | ZFP36L1 | ZFP36 ring finger protein-like 1 | NM_001244698 |
TC1700007262.hg.1 | 4.43 | 0.023 | MAP2K3 | mitogen-activated protein kinase kinase 3 | NM_002756 |
TC0100011384.hg.1 | 2.52 | 0.025 | MAPKAPK2 | mitogen-activated protein kinase-activated protein kinase 2 | NM_004759 |
TC0X00009581.hg.1 | 2.99 | 0.013 | ELK1 | ELK1, member of ETS oncogene family | NM_001114123 |
TC0100016000.hg.1 | 4.15 | 0.004 | MEF2D | myocyte enhancer factor 2D | NM_001271629 |
NF-kB signalling pathway | |||||
TC1900008300.hg.1 | 2.78 | 0.034 | RELB | v-rel avian reticuloendotheliosis viral oncogene homolog B | NM_006509 |
TC1900008279.hg.1 | 5.58 | 0.006 | BCL3 | B-cell CLL/lymphoma 3 | NM_005178 |
TC1600010616.hg.1 | 2.14 | 0.035 | TRADD | TNFRSF1A-associated via death domain | NM_003789 |
TC1100011243.hg.1 | 4.25 | 0.007 | RELA | v-rel avian reticuloendotheliosis viral oncogene homolog A | NM_001145138 |
TC1700010879.hg.1 | 2.36 | 0.026 | MAP3K14 | mitogen-activated protein kinase kinase kinase 14 | NM_003954 |
TC0800012190.hg.1 | 3.65 | 0.018 | SHARPIN | SHANK-associated RH domain interactor | NM_030974 |
TOLL-like receptors signalling pathways | |||||
TC0200008452.hg.1 | 2.85 | 0.024 | MAL | mal, T-cell differentiation protein | NM_002371 |
TC0X00009581.hg.1 | 2.99 | 0.013 | ELK1 | ELK1, member of ETS oncogene family | NM_001114123 |
TC0100011384.hg.1 | 2.52 | 0.025 | MAPKAPK2 | mitogen-activated protein kinase-activated protein kinase 2 | NM_004759 |
TC1000008727.hg.1 | 2.64 | 0.024 | NFKB2 | nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 | NM_001077494 |
TC1700007262.hg.1 | 4.43 | 0.023 | MAP2K3 | mitogen-activated protein kinase kinase 3 | NM_002756 |
TC1100011243.hg.1 | 4.25 | 0.007 | RELA | v-rel avian reticuloendotheliosis viral oncogene homolog A | NM_001145138 |
Jak-Stat signalling pathway | |||||
TC1600009395.hg.1 | 3.76 | 0.010 | SOCS1 | suppressor of cytokine signalling 1 | NM_003745 |
TC1700011903.hg.1 | 4.41 | 0.046 | SOCS3 | suppressor of cytokine signalling 3 | NM_003955 |
TC1900009991.hg.1 | 2.63 | 0.042 | JAK3 | Janus kinase 3 | NM_000215 |
TC1200010950.hg.1 | 2.47 | 0.034 | STAT6 | signal transducer and activator of transcription 6, interleukin-4 induced | NM_001178078 |
PI3K signalling pathway | |||||
TC1900010696.hg.1 | 5.13 | 0.007 | AKT2 | v-akt murine thymoma viral oncogene homolog 2 | NM_001243027 |
TC1100008136.hg.1 | 2.31 | 0.023 | RPS6KB2 | ribosomal protein S6 kinase, 70kDa, polypeptide 2 | NM_003952 |
TC1000007990.hg.1 | 4.92 | 0.020 | DDIT4 | DNA damage inducible transcript 4 | NM_019058 |
TC1000008891.hg.1 | 10.97 | 0.008 | DUSP5 | dual specificity phosphatase 5 | NM_004419 |
TC0700008560.hg.1 | 3.76 | 0.026 | GNB2 | guanine nucleotide binding protein (G protein), beta polypeptide 2 | NM_005273 |
TC1900010009.hg.1 | 3.41 | 0.023 | JUND | jun D proto-oncogene | NM_001286968 |
TC1900007096.hg.1 | 5.16 | 0.032 | JUNB | jun B proto-oncogene | NM_002229 |
TC0600008972.hg.1 | 5.51 | 0.018 | PRDM1 | PR domain containing 1, with ZNF domain | NM_001198 |
mTOR signalling pathway | |||||
TC0300013684.hg.1 | 2.21 | 0.043 | TFRC | transferrin receptor | NM_001128148 |
TC1200007595.hg.1 | 2.88 | 0.023 | SMARCD1 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 1 | NM_003076 |
TC1700011903.hg.1 | 4.41 | 0.046 | SOCS3 | suppressor of cytokine signalling 3 | NM_003955 |
TC2000007283.hg.1 | 2.11 | 0.026 | SRC | SRC proto-oncogene, non-receptor tyrosine kinase | NM_005417 |
TC0400009765.hg.1 | 3.06 | 0.018 | MXD4 | MAX dimerization protein 4 | NM_006454 |
TC0100016000.hg.1 | 4.15 | 0.004 | MEF2D | myocyte enhancer factor 2D | NM_001271629 |
Biological Pathway | Bonferroni Corrected p-Value |
---|---|
Proteoglycan syndecan-mediated signalling events | 0.006 |
Alpha9 beta1 integrin signalling events | 0.020 |
GMCSF-mediated signalling events | 0.025 |
Beta1 integrin cell surface interactions | 0.026 |
IL3-mediated signalling events | 0.027 |
IFN-gamma pathway | 0.028 |
PAR1-mediated thrombin signalling events | 0.031 |
Thrombin/protease-activated receptor (PAR) pathway | 0.032 |
Syndecan-1-mediated signalling events | 0.032 |
Integrin family cell surface interactions | 0.032 |
Plasma membrane oestrogen receptor signalling | 0.033 |
Endothelins | 0.040 |
Signalling events mediated by focal adhesion kinase | 0.040 |
PDGFR-beta signalling pathway | 0.040 |
Arf6 trafficking events | 0.040 |
Class I PI3K signalling events mediated by Akt | 0.040 |
mTOR signalling pathway | 0.040 |
Internalization of ErbB1 | 0.040 |
EGF receptor (ErbB1) signalling pathway | 0.040 |
Class I PI3K signalling events | 0.040 |
Arf6 signalling events | 0.040 |
ErbB1 downstream signalling | 0.040 |
Arf6 downstream pathway | 0.040 |
Insulin Pathway | 0.040 |
Urokinase-type plasminogen activator (uPA) and uPAR-mediated signalling | 0.040 |
S1P1 pathway | 0.040 |
EGFR-dependent Endothelin signalling events | 0.041 |
IGF1 pathway | 0.044 |
ErbB receptor signalling network | 0.045 |
Sphingosine 1-phosphate (S1P) pathway | 0.045 |
IL5-mediated signalling events | 0.045 |
Signalling events mediated by hepatocyte growth factor receptor (c-Met) | 0.047 |
PDGF receptor signalling network | 0.047 |
Nectin adhesion pathway | 0.049 |
Signalling events mediated by VEGFR1 and VEGFR2 | 0.051 |
Glypican 1 network | 0.056 |
Glypican pathway | 0.055 |
VEGF and VEGFR signalling network | 0.055 |
Integrin-linked kinase signalling | 0.053 |
ID | Fold Change | FDR p-Value | Gene Symbol | mRNA Accession | miRNA Targets | Targeted Modulated Genes |
---|---|---|---|---|---|---|
TC0X00010064.hg.1 | −2.03 | 0.049 | FTX | NR_028379 | 64 | 96 |
TC0100018570.hg.1 | −2.64 | 0.034 | HNRNPU-AS1 | NR_026778 | 55 | 161 |
TC2200009240.hg.1 | −2 | 0.042 | MIATNB | NR_110543 | 16 | 11 |
TC1700012077.hg.1 | 2.5 | 0.039 | RP11-498C9.15 | ENST00000582866.1 | 27 | 106 |
TC0100009198.hg.1 | −3.23 | 0.008 | RP4-714D9.5 | ENST00000564623.1 | 6 | 27 |
TC1400006883.hg.1 | 2.74 | 0.018 | RP11-73E17.2 | ENST00000557373.1 | 1 | 4 |
Biological Pathway | Bonferroni Corrected p-Value |
---|---|
Beta1 integrin cell surface interactions | 0.004 |
Integrin family cell surface interactions | 0.006 |
IFN-gamma pathway | 0.008 |
PAR1-mediated thrombin signalling events | 0.008 |
Thrombin/protease-activated receptor (PAR) pathway | 0.009 |
Plasma membrane oestrogen receptor signalling | 0.009 |
Endothelins | 0.009 |
Glypican pathway | 0.014 |
Proteoglycan syndecan-mediated signalling events | 0.016 |
Signalling events mediated by focal adhesion kinase | 0.030 |
Class I PI3K signalling events mediated by Akt | 0.030 |
Internalization of ErbB1 | 0.030 |
Arf6 downstream pathway | 0.030 |
Arf6 trafficking events | 0.030 |
EGF receptor (ErbB1) signalling pathway | 0.030 |
Urokinase-type plasminogen activator (uPA) and uPAR-mediated signalling | 0.030 |
ErbB1 downstream signalling | 0.030 |
S1P1 pathway | 0.030 |
Arf6 signalling events | 0.030 |
mTOR signalling pathway | 0.030 |
Insulin pathway | 0.030 |
PDGFR-beta signalling pathway | 0.030 |
Class I PI3K signalling events | 0.030 |
EGFR-dependent Endothelin signalling events | 0.030 |
IGF1 pathway | 0.031 |
GMCSF-mediated signalling events | 0.031 |
IL5-mediated signalling events | 0.031 |
Signalling events mediated by hepatocyte growth factor receptor (c-Met) | 0.032 |
PDGF receptor signalling network | 0.032 |
IL3-mediated signalling events | 0.032 |
Nectin adhesion pathway | 0.032 |
Signalling events mediated by VEGFR1 and VEGFR2 | 0.033 |
Glypican 1 network | 0.034 |
Syndecan-1-mediated signalling events | 0.035 |
VEGF and VEGFR signalling network | 0.036 |
Alpha9 beta1 integrin signalling events | 0.037 |
Sphingosine 1-phosphate (S1P) pathway | 0.040 |
ErbB receptor signalling network | 0.040 |
Integrin-linked kinase signalling | 0.045 |
Module | miRNAs | Gene |
---|---|---|
M1 | hsa-miR-23c (1.56 up) | CUL3 |
hsa-miR-23b-3p (2.06 up) | CUL3 | |
hsa-miR-23a-3p (1.74 down) | CUL3 | |
hsa-miR-221-3p (2.34 up) | HNRNPA0 | |
hsa-miR-302c-3p (2.48 down) | SOCS3 | |
hsa-miR-221-3p (2.34 up) | SOCS3 | |
M2 | hsa-miR-372-3p (1.63 up) | ANO6 |
M3 | hsa-miR-101-3p (1.80 up) | ATP5G2 |
hsa-miR-137 (2.54 up) | PTGES2 | |
hsa-miR-101-3p (1.80 up) | TERF2 | |
hsa-miR-613 (1.55 down) | TERF2 | |
hsa-miR-221-3p (2.34 up) | TERF2 | |
hsa-miR-206 (2.04 up) | TERF2 | |
M4 | hsa-miR-4735-3p (2.53 up) | ATM |
hsa-miR-101-3p (1.80 up) | NACA | |
hsa-miR-137 (2.54 up) | PCGF5 | |
hsa-miR-101-3p (1.80 up) | SEL1L | |
hsa-miR-101-3p (1.80 up) | SURF4 | |
hsa-miR-613 (1.55 down) | THBS1 | |
hsa-miR-4735-3p (2.53 up) | THBS1 | |
hsa-miR-221-3p (2.34 up) | THBS1 | |
hsa-miR-206 (2.04 up) | THBS1 | |
hsa-miR-18b-5p (1.67 down) | THBS1 | |
hsa-miR-18a-5p (2.32 up) | THBS1 | |
hsa-miR-613 (1.55 down) | VPS45 | |
hsa-miR-206 (2.04 up) | VPS45 | |
M5 | hsa-miR-137 (2.54 up) | AKT2 |
hsa-miR-613 (1.55 down) | JUND | |
hsa-miR-206 (2.04 up) | JUND | |
hsa-miR-520e (1.83 down) | RELA | |
hsa-miR-520d-3p (1.92 down) | RELA | |
hsa-miR-520c-3p (1.52 down) | RELA | |
hsa-miR-520b (1.70 down) | RELA | |
hsa-miR-520a-3p (1.50 down) | RELA | |
hsa-miR-372-3p (1.63 up) | RELA | |
hsa-miR-302e (2.18 down) | RELA | |
hsa-miR-302d-3p (1.84 down) | RELA | |
hsa-miR-302c-3p (2.48 down) | RELA | |
hsa-miR-302b-3p (1.66 down) | RELA | |
hsa-miR-302a-3p (1.58 down) | RELA | |
hsa-miR-137 (2.54 up) | SRC | |
M6 | hsa-miR-23c (1.56 up) | STX12 |
hsa-miR-23b-3p (2.06 up) | STX12 | |
hsa-miR-23a-3p (1.74 down) | STX12 | |
hsa-miR-206 (2.04 up) | STX12 |
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Dolcino, M.; Tinazzi, E.; Puccetti, A.; Lunardi, C. Long Non-Coding RNAs Target Pathogenetically Relevant Genes and Pathways in Rheumatoid Arthritis. Cells 2019, 8, 816. https://doi.org/10.3390/cells8080816
Dolcino M, Tinazzi E, Puccetti A, Lunardi C. Long Non-Coding RNAs Target Pathogenetically Relevant Genes and Pathways in Rheumatoid Arthritis. Cells. 2019; 8(8):816. https://doi.org/10.3390/cells8080816
Chicago/Turabian StyleDolcino, Marzia, Elisa Tinazzi, Antonio Puccetti, and Claudio Lunardi. 2019. "Long Non-Coding RNAs Target Pathogenetically Relevant Genes and Pathways in Rheumatoid Arthritis" Cells 8, no. 8: 816. https://doi.org/10.3390/cells8080816