Background
Methods
Subjects
ID | Age | Sex | Diagnosis | Duration of Sx (months) | Num of Inject* | Pathology Sample | Control Sample |
---|---|---|---|---|---|---|---|
5 | 45 | M | Distal Biceps Rupture | 0.3 | Distal Biceps | Brachialis | |
9 | 48 | M | ECRB tear | 12 | ECRB | EDC | |
10 | 41 | M | Patella Tendon Rupture | 0.1 | Patella | Quad tendon | |
12 | 62 | M | Flexor/Pronator | 18 | 1 | flexor/pronator | Distal Flexor/Pronator |
13 | 62 | F | RTC tear | 48 | 2 | Supraspinatus | Subscap |
15 | 32 | M | Patella Tendon Tear | 3 | Patella tendon | Nl Patellar Tendon | |
16 | 61 | F | RTC tear | 24 | 2 | Supraspinatus | Subscap |
17 | 59 | M | RTC tear | 6 | 1 | Supraspinatus | Subscap |
19 | 45 | M | Flexor/Pronator | 18 | 3 | flexor/pronator | Distal Flexor/Pronator |
20 | 63 | F | RTC tear | 9 | 1 | Supraspinatus | Subscap |
21 | 65 | F | RTC tear | 3 | 1 | Supraspinatus | Biceps |
23 | 64 | F | RTC tear | 8 | 1 | Supraspinatus | Subscap |
24 | 50 | M | RTC tear | 18 | 1 | Supraspinatus | Biceps |
26 | 55 | M | ECRB tear | 4 | ECRB | Distal ECRB | |
27 | 50 | M | RTC tear | 4 | Supraspinatus | Normal RTC | |
28 | 41 | M | Supra tear (PT), OA, Bankart | >24 | Supraspinatus | Biceps Tendon | |
29 | 46 | M | RTC tear, Adhesive Capsulitis | 4 | Supraspinatus | Biceps Tendon | |
30 | 52 | M | ECRB tear | 12 | ECRB | ECRL | |
31 | 66 | M | RTC tear | 6 | Supraspinatus | Subscap | |
32 | 46 | F | RTC tear | 2 | 1 | Supraspinatus | Teres minor |
33 | 44 | M | RTC tear | 6 | 1 | Supraspinatus | Subscap |
34 | 59 | F | RTC tear | 1 | 3 | Supraspinatus | Biceps |
35 | 49 | F | RTC tear | 24 | Supraspinatus | Subscap |
RNA Preparation and Hybridization
Identification of Differentially Expressed Genes
Identification of Significantly Regulated Gene Sets
Histology
Results
Analysis of Tendinopathy Tissue Samples
Patientb
| Cellular Proliferation | Vascular Proliferation | GAG Accumulation | Fiber Disorientation | Total Score |
---|---|---|---|---|---|
5 | 3.5 | 1.5 | 1.5 | 5 | 11.5 |
9 | 5 | 2 | 5 | 5 | 17 |
10 | 4.5 | 5 | 5 | 5 | 19.5 |
12 | 4 | 5 | 1 | 5 | 15 |
13 | 5 | 1 | 3.5 | 5 | 14.5 |
15 | 5 | 5 | 5 | 4.5 | 19.5 |
16 | 3.5 | 2.5 | 2 | 5 | 13 |
17 | 5 | 4.5 | 3 | 5 | 17.5 |
19 | 4.5 | 5 | 3 | 5 | 17.5 |
20 | 5 | 3 | 3 | 5 | 16 |
21 | 5 | 1 | 2 | 5 | 13 |
23 | 4.5 | 3 | 4 | 5 | 16.5 |
24 | 5 | 5 | 3 | 5 | 18 |
26 | 5 | 3 | 5 | 5 | 18 |
27 | 4.5 | 3 | 1 | 5 | 13.5 |
28 | 5 | 1.5 | 5 | 5 | 16.5 |
29 | 5 | 5 | 5 | 5 | 20 |
30 | 4 | 4.5 | 3 | 4.5 | 16 |
31 | 4.5 | 1.5 | 4 | 5 | 15 |
32 | 4.5 | 1.5 | 5 | 5 | 16 |
33 | 5 | 0.5 | 4 | 5 | 14.5 |
34 | 5 | 0.5 | 3 | 5 | 13.5 |
35 | 5 | 5 | 3 | 5 | 18 |
Analysis of Gene Expression
Gene Symbol | Description | p-value | q-value | Fold Change |
---|---|---|---|---|
ADAM12
| A disintegrin and metalloproteinase domain 12 | 1.57E-05 | 2.09E-04 | 5.6 |
AP3M1
| Adaptor-related protein complex 3, mu 1 subunit | 1.24E-03 | 1.91E-03 | 1.7 |
ARL7
| ADP-ribosylation factor-like 7 | 1.43E-03 | 2.11E-03 | 4.0 |
ARPC5
| Actin related protein 2/3 complex, subunit 5 | 3.63E-05 | 2.10E-04 | 1.8 |
ASXL1
| Additional sex combs like 1 (Drosophila) | 1.11E-03 | 1.78E-03 | 1.8 |
ATP6V1A
| ATPase, H+ transporting, lysosomal 70 kDa | 4.18E-05 | 2.10E-04 | 2.5 |
BACE2
| Beta-site APP-cleaving enzyme 2 | 3.17E-06 | 8.01E-05 | 1.9 |
BNC2
| Basonuclin 2 | 1.08E-04 | 3.15E-04 | 2.9 |
CA12
| Carbonic anhydrase XII | 3.57E-05 | 2.10E-04 | 2.8 |
CTHRC1
| Collagen triple helix repeat containing 1 | 5.20E-04 | 1.10E-03 | 4.4 |
DDEF1
| Development and differentiation enhancing factor | 2.83E-05 | 2.10E-04 | 2.1 |
DOCK10
| Dedicator of cytokinesis 10 | 7.91E-03 | 8.11E-03 | 3.3 |
EDIL3
| EGF-like repeats and discoidin I-like domains 3 | 4.80E-03 | 5.34E-03 | 2.9 |
FOXP1
| Forkhead box P1 | 4.67E-05 | 2.10E-04 | 1.7 |
GPR161
| G protein-coupled receptor 161 | 2.76E-04 | 6.89E-04 | 1.9 |
IGFBP3
| Insulin-like growth factor binding protein 3 | 7.29E-03 | 7.67E-03 | 3.5 |
IL13RA2
| Interleukin 13 receptor, alpha 2 | 2.80E-03 | 3.50E-03 | 3.5 |
ILK
| Integrin-linked kinase | 1.00E-04 | 3.15E-04 | 1.6 |
IQGAP1
| IQ motif containing GTPase activating protein 1 | 4.73E-05 | 2.10E-04 | 1.5 |
ITGB1
| Integrin, beta 1 | 3.52E-04 | 8.29E-04 | 1.7 |
ITPKB
| Inositol 1,4,5-trisphosphate 3-kinase B | 7.37E-04 | 1.34E-03 | 2.5 |
JAG1
| Jagged 1 (Alagille syndrome) | 1.90E-03 | 2.52E-03 | 3.1 |
KCNE4
| Potassium voltage-gated channel 4 | 8.19E-03 | 8.19E-03 | 3.4 |
LAMA4
| Laminin, alpha 4 | 6.73E-04 | 1.31E-03 | 3.4 |
LRRC15
| Leucine rich repeat containing 15 | 3.50E-03 | 4.24E-03 | 3.2 |
LRRC17
| Leucine rich repeat containing 17 | 1.74E-03 | 2.40E-03 | 2.8 |
MARCKS
| Myristoylated alanine-rich kinase C substrate | 3.93E-03 | 4.50E-03 | 2.8 |
NOTCH3
| Notch homolog 3 (Drosophila) | 1.65E-03 | 2.36E-03 | 3.6 |
PDIR
| protein disulfide isomerase-related | 4.86E-04 | 1.08E-03 | 2.1 |
POSTN
| Periostin, osteoblast specific factor | 1.10E-04 | 3.15E-04 | 3.5 |
RAP1GDS1
| RAP1, GTP-GDP dissociation stimulator 1 | 1.01E-03 | 1.68E-03 | 2.1 |
S100A10
| S100 calcium binding protein A10 | 1.95E-03 | 2.52E-03 | 2.8 |
SIN3A
| SIN3 homolog A, transcription regulator (yeast) | 9.51E-05 | 3.15E-04 | 1.7 |
SLC2A13
| Solute carrier family 2 13 | 5.41E-03 | 5.85E-03 | 2.8 |
TAOK1
| TAO kinase 1 | 1.51E-04 | 4.03E-04 | 1.7 |
TJP1
| Tight junction protein 1 (zona occludens 1) | 6.87E-04 | 1.31E-03 | 1.6 |
TNC
| Tenascin C (hexabrachion) | 9.20E-05 | 3.15E-04 | 5.3 |
UBE2E3
| Ubiquitin-conjugating enzyme E2E 3 | 8.72E-04 | 1.52E-03 | 3.7 |
WDR1
| WD repeat domain 1 | 4.01E-06 | 8.01E-05 | 1.6 |
WISP1
| WNT1 inducible signaling pathway protein 1 | 3.93E-03 | 4.50E-03 | 3.4 |
NTk* | |
---|---|
Up regulated | |
HSA04110_CELL_CYCLE | 6.52 |
RNA_PROCESSING | 6.44 |
SPINDLE | 6.25 |
HSA04510_FOCAL_ADHESION | 6.10 |
TGFBETA_LATE_UP | 6.02 |
CELL_CYCLE_KEGG | 6.00 |
CELL_CYCLE | 5.94 |
ST_INTEGRIN_SIGNALING_PATHWAY | 5.40 |
COLLAGEN | 5.32 |
RUIZ_TENASCIN_TARGETS | 5.24 |
I_KAPPAB_KINASE_NF_KAPPAB_CASCADE | 5.23 |
MITOSIS | 5.03 |
INOS_ALL_UP | 4.89 |
Down Regulated | |
ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY | -4.99 |
G_PROTEIN_COUPLED_RECEPTOR_ACTIVITY | -5.01 |
ELECTRON_TRANSPORT_CHAIN | -5.21 |
MOOTHA_VOXPHOS | -6.01 |
ION_CHANNEL_ACTIVITY | -6.20 |
SUBSTRATE_SPECIFIC_CHANNEL_ACTIVITY | -6.27 |
Gene Symbol | Description | p-value | q-value | Fold Change |
---|---|---|---|---|
BMP1
| Bone morphogenetic protein 1 | 0.000 | 0.005 | 1.69 |
BMP8B
| Bone morphogenetic protein 8b | 0.002 | 0.011 | 1.79 |
CCL2
| Chemokine (C-C motif) ligand 2 | 0.005 | 0.014 | 1.74 |
CMTM4
| Chemokine-like factor super family 4 | 0.008 | 0.017 | 1.98 |
CMTM6
| Chemokine-like factor super family 6 | 0.014 | 0.023 | 1.37 |
IFNGR1
| Interferon gamma receptor 1 | 0.027 | 0.034 | 1.42 |
IL13RA2
| Interleukin 13 receptor, alpha 2 | 0.003 | 0.011 | 3.48 |
IL17D
| Interleukin 17D | 0.008 | 0.017 | 0.54 |
IL6R
| Interleukin 6 receptor | 0.026 | 0.034 | 0.73 |
LEPR
| Leptin receptor | 0.028 | 0.034 | 0.49 |
OSMR
| Oncostatin M receptor | 0.038 | 0.043 | 1.81 |
SP110
| SP110 nuclear body protein | 0.010 | 0.019 | 1.51 |
STAT2
| Signal transducer and activator of transcription 2 | 0.051 | 0.054 | 1.4 |
STAT3
| Signal transducer and activator of transcription 3 | 0.004 | 0.013 | 1.87 |
TXLNA
| Taxilin | 0.001 | 0.006 | 1.39 |
Gene Symbol | Description | p-value | q-value | Fold Change | |
---|---|---|---|---|---|
Regulated | |||||
MMP2
| Matrix metallopeptidase 2 | Expressed | 7.42E-03 | 4.82E-02 | 1.8 |
MMP3
| Matrix metallopeptidase 3 | Expressed | 5.50E-02 | 2.38E-01 | 0.3 |
MMP14
| Matrix metallopeptidase 14 | Expressed | 1.79E-03 | 1.66E-02 | 1.9 |
MMP19
| Matrix metallopeptidase 19 | Expressed | 1.91E-03 | 1.66E-02 | 3.4 |
Not Regulated | |||||
MMP28
| Matrix metallopeptidase 28 | Expressed | 0.09 | 0.30 | 1.4 |
TIMP1
| TIMP metallopeptidase inhibitor 1 | Expressed | 0.10 | 0.30 | 1.6 |
TIMP2
| TIMP metallopeptidase inhibitor 2 | Expressed | 0.37 | 0.50 | 1.1 |
TIMP3
| TIMP metallopeptidase inhibitor 3 | Expressed | 0.26 | 0.49 | 0.9 |
TIMP4
| TIMP metallopeptidase inhibitor 4 | Expressed | 0.71 | 0.80 | 0.9 |
Expressed below limited of detection | |||||
MMP1
| Matrix metallopeptidase 1 | - | 0.96 | 0.96 | 1.0 |
MMP7
| Matrix metallopeptidase 7 | - | 0.34 | 0.49 | 0.8 |
MMP8
| Matrix metallopeptidase 8 | - | 0.81 | 0.84 | 0.8 |
MMP9
| Matrix metallopeptidase 9 | - | 0.00 | 0.02 | 3.2 |
MMP10
| Matrix metallopeptidase 10 | - | 0.08 | 0.30 | 0.8 |
MMP12
| Matrix metallopeptidase 12 | - | 0.79 | 0.84 | 0.9 |
MMP13
| Matrix metallopeptidase 13 | - | 0.03 | 0.14 | 2.6 |
MMP15
| Matrix metallopeptidase 15 | - | 0.15 | 0.35 | 0.5 |
MMP16
| Matrix metallopeptidase 16 | - | 0.57 | 0.67 | 0.6 |
MMP17
| Matrix metallopeptidase 17 | - | 0.56 | 0.67 | 0.8 |
MMP20
| Matrix metallopeptidase 20 | - | 0.53 | 0.67 | 0.7 |
MMP21
| Matrix metallopeptidase 21 | - | 0.13 | 0.33 | 1.5 |
MMP23A/B
| Matrix metallopeptidase 23A/B | - | 0.34 | 0.49 | 0.8 |
MMP24
| Matrix metallopeptidase 2 | - | 0.29 | 0.49 | 0.6 |
MMP25
| Matrix metallopeptidase 25 | - | 0.18 | 0.40 | 0.7 |
MMP26
| Matrix metallopeptidase 26 | - | 0.34 | 0.49 | 0.8 |
MMP27
| Matrix metallopeptidase 27 | - | 0.33 | 0.49 | 0.8 |
Gene Symbol | Description | p-value | q-value | Fold Change | |
---|---|---|---|---|---|
Regulated | |||||
COL1A1
| Collagen, type I, alpha 1 | Expressed | 9.37E-03 | 3.96E-02 | 1.7 |
COL1A2
| Collagen, type I, alpha 2 | Expressed | 4.45E-03 | 3.16E-02 | 1.6 |
COL3A1
| Collagen, type III, alpha 1 | Expressed | 1.50E-02 | 4.28E-02 | 2.0 |
COL4A1
| Collagen, type IV, alpha 1 | Expressed | 1.91E-02 | 4.53E-02 | 2.7 |
COL4A2
| Collagen, type IV, alpha 2 | Expressed | 6.09E-03 | 3.16E-02 | 2.3 |
COL5A1
| Collagen, type V, alpha 1 | Expressed | 1.20E-02 | 4.28E-02 | 2.0 |
COL5A2
| Collagen, type V, alpha 2 | Expressed | 3.99E-03 | 3.16E-02 | 2.1 |
COL5A3
| Collagen, type V, alpha 3 | Expressed | 3.02E-03 | 3.16E-02 | 2.0 |
COL6A1
| Collagen, type VI, alpha 1 | Expressed | 2.93E-02 | 6.18E-02 | 1.8 |
COL6A2
| Collagen, type VI, alpha 2 | Expressed | 3.62E-02 | 6.89E-02 | 1.8 |
COL6A3
| Collagen, type VI, alpha 3 | Expressed | 5.45E-03 | 3.16E-02 | 1.7 |
COL8A1
| Collagen, type VIII, alpha 1 | Expressed | 2.49E-02 | 5.57E-02 | 2.0 |
COL8A2
| Collagen, type VIII, alpha 2 | Expressed | 1.48E-02 | 4.28E-02 | 1.8 |
COL10A1
| Collagen, type X, alpha 1 | Expressed | 1.69E-02 | 4.28E-02 | 2.1 |
COL12A1
| Collagen, type XII, alpha 1 | Expressed | 4.10E-03 | 3.16E-02 | 2.1 |
COL18A1
| Collagen, type XVIII, alpha 1 | Expressed | 6.65E-03 | 3.16E-02 | 2.2 |
COL27A1
| Collagen, type XXVII, alpha 1 | Expressed | 1.20E-03 | 3.16E-02 | 2.5 |
Not Regulated | |||||
COL7A1
| Collagen, type VII, alpha 1 | Expressed | 0.96 | 0.96 | 1.0 |
COL11A1
| Collagen, type XI, alpha 1 | Expressed | 0.58 | 0.71 | 1.2 |
COL15A1
| Collagen, type XV, alpha 1 | Expressed | 0.51 | 0.64 | 1.2 |
COL16A1
| Collagen, type XVI, alpha 1 | Expressed | 0.12 | 0.19 | 1.4 |
COL21A1
| Collagen, type XXI, alpha 1 | Expressed | 0.34 | 0.45 | 1.4 |
Expressed below limited of detection | |||||
COL2A1
| Collagen, type II, alpha 1 | - | 0.21 | 0.31 | 0.5 |
COL4A3
| Collagen, type IV, alpha 3 | - | 0.15 | 0.23 | 0.6 |
COL4A4
| Collagen, type IV, alpha 4 | - | 0.90 | 0.96 | 1.0 |
COL4A5
| Collagen, type IV, alpha 5 | - | 0.71 | 0.84 | 0.9 |
COL4A6
| Collagen, type IV, alpha 6 | - | 0.94 | 0.96 | 1.0 |
COL9A1
| Collagen, type IX, alpha 1 | - | 0.94 | 0.96 | 1.0 |
COL9A2
| Collagen, type IX, alpha 2 | - | 0.05 | 0.08 | 1.9 |
COL11A2
| Collagen, type XI, alpha 2 | - | 0.12 | 0.19 | 0.7 |
COL13A1
| Collagen, type XIII, alpha 1 | - | 0.08 | 0.13 | 2.0 |
COL14A1
| Collagen, type XIV, alpha 1 | - | 0.02 | 0.04 | 1.8 |
COL17A1
| Collagen, type XVII, alpha 1 | - | 0.33 | 0.45 | 1.3 |
COL19A1
| Collagen, type XIX, alpha 1 | - | 0.02 | 0.04 | 0.5 |
COL22A1
| Collagen, type XXII, alpha 1 | - | 0.03 | 0.07 | 0.5 |
COL23A1
| Collagen, type XXIII, alpha 1 | - | 0.75 | 0.84 | 1.0 |
COL24A1
| Collagen, type XXIV, alpha 1 | - | 0.33 | 0.45 | 1.3 |
COL25A1
| Collagen, type XXV, alpha 1 | - | 0.76 | 0.84 | 0.9 |
Gene Symbol | Description | pValue | q-value | Fold Change |
---|---|---|---|---|
ABL2
| v-abl Abelson leukemia viral oncogene homolog 2 | 4.79E-03 | 7.83E-03 | 31.0 |
BMPR2
| Bone morphogenetic protein receptor, type II | 4.10E-03 | 7.83E-03 | 27.0 |
CAV2
| Caveolin 2 | 1.22E-02 | 1.44E-02 | 43.0 |
CDK6
| Cyclin-dependent kinase 6 | 1.37E-02 | 1.53E-02 | 24.0 |
CSNK1D
| Casein kinase 1, delta | 5.21E-03 | 8.13E-03 | 19.0 |
CSNK1G1
| Casein kinase 1, gamma 1 | 8.18E-03 | 1.03E-02 | 40.0 |
DCLK1
| Doublecortin-like kinase 1 | 3.78E-03 | 7.83E-03 | 28.0 |
EML4
| Echinoderm microtubule associated protein like 4 | 9.69E-04 | 3.15E-03 | 41.0 |
EPS8
| Epidermal growth factor receptor substrate 8 | 1.96E-04 | 1.67E-03 | 9.0 |
FGFR1
| Fibroblast growth factor receptor 1 | 5.64E-03 | 8.46E-03 | 1.7 |
ILK
| Integrin-linked kinase | 1.00E-04 | 1.67E-03 | 1.6 |
JAK3
| Janus kinase 3 | 4.62E-03 | 7.83E-03 | 1.8 |
KIAA0220
| PI-3-kinase-related kinase SMG-1 | 2.70E-03 | 7.02E-03 | 1.6 |
KIAA0999
| KIAA0999 protein | 1.62E-03 | 4.86E-03 | 2.1 |
MAP3K2
| Mitogen-activated protein kinase kinase kinase 2 | 4.82E-03 | 7.83E-03 | 1.8 |
MAP4K5
| Mitogen-activated protein kinase kinase kinase 5 | 1.31E-02 | 1.50E-02 | 1.9 |
MAPK8
| Mitogen-activated protein kinase 8 | 1.42E-02 | 1.54E-02 | 2.0 |
NAGK
| N-acetylglucosamine kinase | 4.16E-03 | 7.83E-03 | 1.8 |
PALM2-AKAP2
| A kinase (PRKA) anchor protein 2 | 2.31E-02 | 2.37E-02 | 1.9 |
PANK2
| Pantothenate kinase 2 | 6.39E-04 | 2.67E-03 | 1.6 |
PAPSS1
| 3'-phosphoadenosine 5'-phosphosulfate synthase 1 | 2.35E-04 | 1.67E-03 | 1.8 |
PDLIM5
| PDZ and LIM domain 5 | 8.94E-03 | 1.09E-02 | 1.9 |
PFTK1
| PFTAIRE protein kinase 1 | 4.74E-03 | 7.83E-03 | 1.6 |
PGAM1
| Phosphoglycerate mutase 1 (brain) | 4.81E-04 | 2.35E-03 | 1.6 |
PI4K2B
| Phosphatidylinositol 4-kinase type 2 beta | 7.80E-03 | 1.02E-02 | 1.7 |
PIK3C2A
| Phosphoinositide-3-kinase, class 2, alpha | 2.28E-02 | 2.37E-02 | 1.5 |
PIP4K2A
| Phosphatidylinositol-5-phosphate 4-kinase, Iia | 7.52E-04 | 2.67E-03 | 1.5 |
PRKAA1
| Protein kinase, AMP-activated, alpha 1 | 5.32E-02 | 5.32E-02 | 1.7 |
PRKD1
| Protein kinase D1 | 7.86E-03 | 1.02E-02 | 1.8 |
PTK9
| Twinfilin, actin-binding protein, homolog 1 | 1.62E-04 | 1.67E-03 | 1.7 |
RIPK2
| Receptor-interacting serine-threonine kinase 2 | 1.84E-03 | 5.11E-03 | 1.6 |
RIPK5
| Receptor interacting protein kinase 5 | 5.91E-03 | 8.53E-03 | 1.7 |
SGMS2
| Sphingomyelin synthase 2 | 3.38E-03 | 7.76E-03 | 2.3 |
SHC1
| Src homology 2 domain containing protein 1 | 2.99E-04 | 1.67E-03 | 1.7 |
SOCS3
| Suppressor of cytokine signaling 3 | 3.07E-03 | 7.48E-03 | 1.7 |
SSA2
| TROVE domain family, member 2 | 2.72E-04 | 1.67E-03 | 1.6 |
TAOK1
| TAO kinase 1 | 1.51E-04 | 1.67E-03 | 1.7 |
TRIM27
| Tripartite motif-containing 27 | 6.94E-04 | 2.67E-03 | 1.6 |
TTN
| Titin | 6.67E-03 | 9.29E-03 | 0.2 |