Details for gene set GO_SKELETAL_SYSTEM_MORPHOGENESIS[GSEA]

Table: GSEA Results Summary

Dataset	NS50832_collapsed_to_symbols.NS50832.cls #558AP2_versus_S78.NS50832.cls #558AP2_versus_S78_repos
Phenotype	NS50832.cls#558AP2_versus_S78_repos
Upregulated in class	1
GeneSet	GO_SKELETAL_SYSTEM_MORPHOGENESIS
Enrichment Score (ES)	0.58721775
Normalized Enrichment Score (NES)	1.9539124
Nominal p-value	0.0
FDR q-value	0.021680193
FWER p-Value	0.077

Fig 1: Enrichment plot: GO_SKELETAL_SYSTEM_MORPHOGENESIS   
Profile of the Running ES Score & Positions of GeneSet Members on the Rank Ordered List

Table: GSEA details [plain text format]

	PROBE	GENE SYMBOL	GENE_TITLE	RANK IN GENE LIST	RANK METRIC SCORE	RUNNING ES	CORE ENRICHMENT
1	MSX2	MSX2 Entrez,  Source	msh homeobox homolog 2 (Drosophila)	79	3.875	0.0373	Yes
2	DSCAML1	DSCAML1 Entrez,  Source	Down syndrome cell adhesion molecule like 1	83	3.793	0.0774	Yes
3	CER1	CER1 Entrez,  Source	cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis)	106	3.534	0.1138	Yes
4	SIX1	SIX1 Entrez,  Source	sine oculis homeobox homolog 1 (Drosophila)	113	3.493	0.1506	Yes
5	HHIP	HHIP Entrez,  Source	hedgehog interacting protein	128	3.347	0.1854	Yes
6	OSR2	OSR2 Entrez,  Source	odd-skipped related 2 (Drosophila)	138	3.259	0.2196	Yes
7	SP5	SP5 Entrez,  Source	Sp5 transcription factor	140	3.246	0.2539	Yes
8	SIX2	SIX2 Entrez,  Source	sine oculis homeobox homolog 2 (Drosophila)	161	3.101	0.2859	Yes
9	ALX1			239	2.734	0.3112	Yes
10	TFAP2A	TFAP2A Entrez,  Source	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	264	2.598	0.3376	Yes
11	IRX5	IRX5 Entrez,  Source	iroquois homeobox protein 5	353	2.302	0.3578	Yes
12	LTF	LTF Entrez,  Source	lactotransferrin	364	2.257	0.3812	Yes
13	CSGALNACT1			409	2.118	0.4016	Yes
14	UNCX			451	2.014	0.4210	Yes
15	P2RX7	P2RX7 Entrez,  Source	purinergic receptor P2X, ligand-gated ion channel, 7	532	1.839	0.4366	Yes
16	BMP4	BMP4 Entrez,  Source	bone morphogenetic protein 4	620	1.680	0.4503	Yes
17	T	T Entrez,  Source	T, brachyury homolog (mouse)	641	1.634	0.4667	Yes
18	TWIST1	TWIST1 Entrez,  Source	twist homolog 1 (acrocephalosyndactyly 3; Saethre-Chotzen syndrome) (Drosophila)	653	1.619	0.4833	Yes
19	TGFB2	TGFB2 Entrez,  Source	transforming growth factor, beta 2	657	1.613	0.5003	Yes
20	HAS2	HAS2 Entrez,  Source	hyaluronan synthase 2	675	1.582	0.5162	Yes
21	COMP	COMP Entrez,  Source	cartilage oligomeric matrix protein	773	1.463	0.5271	Yes
22	TBX1	TBX1 Entrez,  Source	T-box 1	892	1.305	0.5353	Yes
23	FREM1	FREM1 Entrez,  Source	FRAS1 related extracellular matrix 1	965	1.234	0.5449	Yes
24	MSX1	MSX1 Entrez,  Source	msh homeobox homolog 1 (Drosophila)	1017	1.192	0.5551	Yes
25	NKX3-2			1119	1.103	0.5620	Yes
26	FGF4	FGF4 Entrez,  Source	fibroblast growth factor 4 (heparin secretory transforming protein 1, Kaposi sarcoma oncogene)	1178	1.049	0.5703	Yes
27	PAX5	PAX5 Entrez,  Source	paired box gene 5 (B-cell lineage specific activator)	1298	0.976	0.5749	Yes
28	INSIG1	INSIG1 Entrez,  Source	insulin induced gene 1	1362	0.931	0.5818	Yes
29	RIPPLY2			1445	0.883	0.5872	Yes
30	HYAL1	HYAL1 Entrez,  Source	hyaluronoglucosaminidase 1	1720	0.765	0.5822	No
31	SHOX2	SHOX2 Entrez,  Source	short stature homeobox 2	2010	0.646	0.5752	No
32	TGFB1	TGFB1 Entrez,  Source	transforming growth factor, beta 1 (Camurati-Engelmann disease)	2411	0.533	0.5616	No
33	MATN1	MATN1 Entrez,  Source	matrilin 1, cartilage matrix protein	2463	0.519	0.5647	No
34	ACP5	ACP5 Entrez,  Source	acid phosphatase 5, tartrate resistant	2785	0.442	0.5540	No
35	WNT9A	WNT9A Entrez,  Source	wingless-type MMTV integration site family, member 9A	3047	0.388	0.5456	No
36	FGFR3	FGFR3 Entrez,  Source	fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism)	3245	0.352	0.5398	No
37	PHOSPHO1	PHOSPHO1 Entrez,  Source	phosphatase, orphan 1	3311	0.342	0.5403	No
38	TEK	TEK Entrez,  Source	TEK tyrosine kinase, endothelial (venous malformations, multiple cutaneous and mucosal)	3376	0.332	0.5408	No
39	TULP3	TULP3 Entrez,  Source	tubby like protein 3	3496	0.310	0.5384	No
40	NODAL	NODAL Entrez,  Source	nodal homolog (mouse)	3518	0.308	0.5406	No
41	MMP2	MMP2 Entrez,  Source	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	3574	0.299	0.5412	No
42	THBS3	THBS3 Entrez,  Source	thrombospondin 3	3689	0.286	0.5387	No
43	DHRS3	DHRS3 Entrez,  Source	dehydrogenase/reductase (SDR family) member 3	3752	0.277	0.5387	No
44	TGFBR2	TGFBR2 Entrez,  Source	transforming growth factor, beta receptor II (70/80kDa)	3829	0.267	0.5379	No
45	NAB2	NAB2 Entrez,  Source	NGFI-A binding protein 2 (EGR1 binding protein 2)	4006	0.247	0.5320	No
46	WWOX	WWOX Entrez,  Source	WW domain containing oxidoreductase	4107	0.238	0.5298	No
47	STC1	STC1 Entrez,  Source	stanniocalcin 1	4551	0.201	0.5106	No
48	EYA1	EYA1 Entrez,  Source	eyes absent homolog 1 (Drosophila)	4596	0.198	0.5106	No
49	IFT80	IFT80 Entrez,  Source	intraflagellar transport 80 homolog (Chlamydomonas)	4601	0.198	0.5125	No
50	SFRP2	SFRP2 Entrez,  Source	secreted frizzled-related protein 2	4747	0.188	0.5076	No
51	FLVCR1			4807	0.185	0.5067	No
52	COL1A1	COL1A1 Entrez,  Source	collagen, type I, alpha 1	5261	0.157	0.4866	No
53	LRP5	LRP5 Entrez,  Source	low density lipoprotein receptor-related protein 5	5603	0.140	0.4717	No
54	THRA	THRA Entrez,  Source	thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian)	5639	0.138	0.4715	No
55	MMP14	MMP14 Entrez,  Source	matrix metallopeptidase 14 (membrane-inserted)	5833	0.129	0.4636	No
56	NDST1	NDST1 Entrez,  Source	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	5841	0.129	0.4646	No
57	NOG	NOG Entrez,  Source	noggin	5925	0.125	0.4620	No
58	COL27A1	COL27A1 Entrez,  Source	collagen, type XXVII, alpha 1	5964	0.123	0.4615	No
59	BMPR2	BMPR2 Entrez,  Source	bone morphogenetic protein receptor, type II (serine/threonine kinase)	6127	0.117	0.4549	No
60	COL11A1	COL11A1 Entrez,  Source	collagen, type XI, alpha 1	6410	0.105	0.4425	No
61	NLE1	NLE1 Entrez,  Source	notchless homolog 1 (Drosophila)	6454	0.104	0.4416	No
62	SLC39A3	SLC39A3 Entrez,  Source	solute carrier family 39 (zinc transporter), member 3	6506	0.102	0.4402	No
63	HYAL2	HYAL2 Entrez,  Source	hyaluronoglucosaminidase 2	6597	0.099	0.4369	No
64	AXIN2	AXIN2 Entrez,  Source	axin 2 (conductin, axil)	6645	0.098	0.4357	No
65	SKI	SKI Entrez,  Source	v-ski sarcoma viral oncogene homolog (avian)	6684	0.096	0.4349	No
66	GNAS	GNAS Entrez,  Source	GNAS complex locus	6705	0.096	0.4350	No
67	TGFBR1	TGFBR1 Entrez,  Source	transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kDa)	6771	0.094	0.4328	No
68	FGFR1	FGFR1 Entrez,  Source	fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome)	6849	0.091	0.4301	No
69	EIF4A3			6987	0.087	0.4245	No
70	BMP6	BMP6 Entrez,  Source	bone morphogenetic protein 6	7206	0.081	0.4148	No
71	SLC39A1	SLC39A1 Entrez,  Source	solute carrier family 39 (zinc transporter), member 1	7402	0.075	0.4063	No
72	ALPL	ALPL Entrez,  Source	alkaline phosphatase, liver/bone/kidney	7492	0.072	0.4028	No
73	ACVR2B	ACVR2B Entrez,  Source	activin A receptor, type IIB	7740	0.066	0.3916	No
74	WDR48	WDR48 Entrez,  Source	WD repeat domain 48	7747	0.065	0.3920	No
75	WDR19	WDR19 Entrez,  Source	WD repeat domain 19	7872	0.062	0.3867	No
76	BMP7	BMP7 Entrez,  Source	bone morphogenetic protein 7 (osteogenic protein 1)	7994	0.059	0.3815	No
77	SMAD3	SMAD3 Entrez,  Source	SMAD, mothers against DPP homolog 3 (Drosophila)	8112	0.055	0.3765	No
78	FUZ	FUZ Entrez,  Source	fuzzy homolog (Drosophila)	8211	0.053	0.3724	No
79	ZFAND5	ZFAND5 Entrez,  Source	zinc finger, AN1-type domain 5	8578	0.044	0.3553	No
80	MYCN	MYCN Entrez,  Source	v-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)	8781	0.039	0.3460	No
81	PKD1	PKD1 Entrez,  Source	polycystic kidney disease 1 (autosomal dominant)	8829	0.038	0.3441	No
82	MAPK14	MAPK14 Entrez,  Source	mitogen-activated protein kinase 14	8899	0.036	0.3412	No
83	CARM1	CARM1 Entrez,  Source	coactivator-associated arginine methyltransferase 1	8926	0.036	0.3403	No
84	FGFR2	FGFR2 Entrez,  Source	ffer syndrome, Jackson-Weiss syndrome)	9005	0.033	0.3370	No
85	MTHFD1L	MTHFD1L Entrez,  Source	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	9034	0.033	0.3360	No
86	BMP1	BMP1 Entrez,  Source	bone morphogenetic protein 1	9077	0.032	0.3343	No
87	INPPL1	INPPL1 Entrez,  Source	inositol polyphosphate phosphatase-like 1	9159	0.029	0.3307	No
88	AXIN1	AXIN1 Entrez,  Source	axin 1	9278	0.026	0.3253	No
89	SERPINH1	SERPINH1 Entrez,  Source	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	9342	0.025	0.3226	No
90	GSC	GSC Entrez,  Source	goosecoid	9498	0.021	0.3153	No
91	SIX4	SIX4 Entrez,  Source	sine oculis homeobox homolog 4 (Drosophila)	9577	0.020	0.3118	No
92	SOX11	SOX11 Entrez,  Source	SRY (sex determining region Y)-box 11	9608	0.019	0.3106	No
93	CSRNP1			9618	0.018	0.3103	No
94	MTHFD1	MTHFD1 Entrez,  Source	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	9669	0.017	0.3081	No
95	MEGF8	MEGF8 Entrez,  Source	multiple EGF-like-domains 8	9768	0.015	0.3036	No
96	SFRP1	SFRP1 Entrez,  Source	secreted frizzled-related protein 1	9775	0.014	0.3034	No
97	CTNNB1	CTNNB1 Entrez,  Source	catenin (cadherin-associated protein), beta 1, 88kDa	9928	0.011	0.2962	No
98	PRKRA	PRKRA Entrez,  Source	protein kinase, interferon-inducible double stranded RNA dependent activator	9988	0.009	0.2935	No
99	DLG1	DLG1 Entrez,  Source	discs, large homolog 1 (Drosophila)	10147	0.005	0.2860	No
100	WNT10B	WNT10B Entrez,  Source	wingless-type MMTV integration site family, member 10B	10155	0.005	0.2857	No
101	ROR2	ROR2 Entrez,  Source	receptor tyrosine kinase-like orphan receptor 2	10254	0.003	0.2810	No
102	PLEKHA1	PLEKHA1 Entrez,  Source	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1	10312	0.001	0.2783	No
103	SETD2	SETD2 Entrez,  Source	SET domain containing 2	10457	-0.002	0.2714	No
104	RARG	RARG Entrez,  Source	retinoic acid receptor, gamma	10913	-0.015	0.2497	No
105	GLG1	GLG1 Entrez,  Source	golgi apparatus protein 1	10922	-0.015	0.2495	No
106	NIPBL	NIPBL Entrez,  Source	Nipped-B homolog (Drosophila)	11225	-0.023	0.2353	No
107	CHSY1	CHSY1 Entrez,  Source	carbohydrate (chondroitin) synthase 1	11531	-0.032	0.2210	No
108	PCGF2	PCGF2 Entrez,  Source	polycomb group ring finger 2	11658	-0.036	0.2153	No
109	PSEN1	PSEN1 Entrez,  Source	presenilin 1 (Alzheimer disease 3)	11725	-0.038	0.2125	No
110	IMPAD1	IMPAD1 Entrez,  Source	inositol monophosphatase domain containing 1	11740	-0.039	0.2123	No
111	SMAD2	SMAD2 Entrez,  Source	SMAD, mothers against DPP homolog 2 (Drosophila)	11831	-0.042	0.2084	No
112	COL13A1	COL13A1 Entrez,  Source	collagen, type XIII, alpha 1	11906	-0.044	0.2053	No
113	NAB1	NAB1 Entrez,  Source	NGFI-A binding protein 1 (EGR1 binding protein 1)	12060	-0.049	0.1985	No
114	NPPC	NPPC Entrez,  Source	natriuretic peptide precursor C	12065	-0.049	0.1988	No
115	TCF15	TCF15 Entrez,  Source	transcription factor 15 (basic helix-loop-helix)	12119	-0.051	0.1968	No
116	PPARGC1B	PPARGC1B Entrez,  Source	peroxisome proliferative activated receptor, gamma, coactivator 1, beta	12685	-0.071	0.1705	No
117	IFT140	IFT140 Entrez,  Source	intraflagellar transport 140 homolog (Chlamydomonas)	12725	-0.073	0.1694	No
118	OSR1	OSR1 Entrez,  Source	odd-skipped related 1 (Drosophila)	13164	-0.091	0.1493	No
119	SATB2	SATB2 Entrez,  Source	SATB family member 2	13285	-0.097	0.1446	No
120	MDFI	MDFI Entrez,  Source	MyoD family inhibitor	13753	-0.119	0.1234	No
121	MEF2D	MEF2D Entrez,  Source	MADS box transcription enhancer factor 2, polypeptide D (myocyte enhancer factor 2D)	13818	-0.122	0.1216	No
122	GRHL2	GRHL2 Entrez,  Source	grainyhead-like 2 (Drosophila)	13840	-0.124	0.1219	No
123	RAB23	RAB23 Entrez,  Source	RAB23, member RAS oncogene family	13915	-0.128	0.1198	No
124	ANKRD11	ANKRD11 Entrez,  Source	ankyrin repeat domain 11	14015	-0.133	0.1164	No
125	CHST11	CHST11 Entrez,  Source	carbohydrate (chondroitin 4) sulfotransferase 11	14514	-0.167	0.0943	No
126	GLI3	GLI3 Entrez,  Source	GLI-Kruppel family member GLI3 (Greig cephalopolysyndactyly syndrome)	14554	-0.170	0.0942	No
127	MMP16	MMP16 Entrez,  Source	matrix metallopeptidase 16 (membrane-inserted)	14571	-0.171	0.0953	No
128	CYP26B1	CYP26B1 Entrez,  Source	cytochrome P450, family 26, subfamily B, polypeptide 1	14650	-0.178	0.0934	No
129	LHX1	LHX1 Entrez,  Source	LIM homeobox 1	14679	-0.181	0.0940	No
130	CTGF	CTGF Entrez,  Source	connective tissue growth factor	14702	-0.182	0.0949	No
131	MED12	MED12 Entrez,  Source	mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)	14973	-0.202	0.0840	No
132	RDH10	RDH10 Entrez,  Source	retinol dehydrogenase 10 (all-trans)	15101	-0.211	0.0802	No
133	COL2A1	COL2A1 Entrez,  Source	collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)	15236	-0.224	0.0761	No
134	SGPL1	SGPL1 Entrez,  Source	sphingosine-1-phosphate lyase 1	15313	-0.232	0.0749	No
135	PEX7	PEX7 Entrez,  Source	peroxisomal biogenesis factor 7	15531	-0.251	0.0672	No
136	FOXC2	FOXC2 Entrez,  Source	forkhead box C2 (MFH-1, mesenchyme forkhead 1)	15651	-0.264	0.0643	No
137	INSIG2	INSIG2 Entrez,  Source	insulin induced gene 2	15875	-0.291	0.0567	No
138	TIPARP	TIPARP Entrez,  Source	TCDD-inducible poly(ADP-ribose) polymerase	15886	-0.292	0.0593	No
139	RAB33B	RAB33B Entrez,  Source	RAB33B, member RAS oncogene family	16034	-0.310	0.0555	No
140	FBN2	FBN2 Entrez,  Source	fibrillin 2 (congenital contractural arachnodactyly)	16089	-0.318	0.0563	No
141	RARB	RARB Entrez,  Source	retinoic acid receptor, beta	16104	-0.320	0.0590	No
142	RARA	RARA Entrez,  Source	retinoic acid receptor, alpha	16221	-0.336	0.0570	No
143	COL10A1	COL10A1 Entrez,  Source	collagen, type X, alpha 1(Schmid metaphyseal chondrodysplasia)	16619	-0.398	0.0422	No
144	ARID5B	ARID5B Entrez,  Source	AT rich interactive domain 5B (MRF1-like)	16832	-0.431	0.0366	No
145	ZEB1			16899	-0.442	0.0381	No
146	RUNX2	RUNX2 Entrez,  Source	runt-related transcription factor 2	17588	-0.605	0.0115	No
147	PAPPA2	PAPPA2 Entrez,  Source	pappalysin 2	17822	-0.670	0.0074	No
148	SOX9	SOX9 Entrez,  Source	SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal)	18063	-0.745	0.0038	No
149	FMN1	FMN1 Entrez,  Source	formin 1	18127	-0.763	0.0089	No
150	BMPR1B	BMPR1B Entrez,  Source	bone morphogenetic protein receptor, type IB	19537	-1.438	-0.0435	No
151	MEF2C	MEF2C Entrez,  Source	MADS box transcription enhancer factor 2, polypeptide C (myocyte enhancer factor 2C)	19610	-1.499	-0.0311	No
152	SPEF2			19637	-1.525	-0.0161	No
153	PDGFRA	PDGFRA Entrez,  Source	platelet-derived growth factor receptor, alpha polypeptide	19651	-1.536	-0.0005	No
154	TBX15	TBX15 Entrez,  Source	T-box 15	19765	-1.632	0.0114	No
155	TGFB3	TGFB3 Entrez,  Source	transforming growth factor, beta 3	19788	-1.653	0.0279	No
156	FGF18	FGF18 Entrez,  Source	fibroblast growth factor 18	20548	-2.809	0.0213	No

Fig 2: GO_SKELETAL_SYSTEM_MORPHOGENESIS   
Blue-Pink O' Gram in the Space of the Analyzed GeneSet

Fig 3: GO_SKELETAL_SYSTEM_MORPHOGENESIS: Random ES distribution   
Gene set null distribution of ES for GO_SKELETAL_SYSTEM_MORPHOGENESIS