Microarray technology reveals potentially novel genes and pathways involved in non-functioning pituitary adenomas

X Qiao; H Wang; X Wang; B Zhao; J Liu

Open Access

Microarray technology reveals potentially novel genes and pathways involved in non-functioning pituitary adenomas

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| Dec 31, 2016

Balkan Journal of Medical Genetics

Volume 19 (2016): Issue 2 (December 2016)

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Published Online: Dec 31, 2016

Page range: 5 - 16

DOI: https://doi.org/10.1515/bjmg-2016-0030

Keywords
Differentially expressed genes (DEGs), Functional enrichment analysis, Microarray, Non-functioning pituitary adenomas (NFPAs), Protein-protein interaction (PPI)

© 2016 Qiao X, Wang H, Wang X, Zhao B, Liu J

This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Cluster analysis of DEGs. DEGs: differentially expressed genes; T: tumor samples; N: healthy normal samples. Cluster analysis was performed both at gene level (vertical) and sample level (horizontal).

The MAPK signaling pathway. Genes down-regulated in NFPAs are shown in green, while up-regulated genes are in red.

The p53 signaling pathway. Genes down-regulated in NFPAs are shown in green, while up-regulated genes are in red.

The TGFβ signaling pathway. Genes down-regulated in NFPAs are shown in green, while up-regulated genes are in red.

Jak-STAT signaling pathway. Genes down-regulated in NFPAs are shown in green, while up-regulated genes are in red.

The whole PPI network of DEGs. Red nodes represent the genes up-regulated in NFPAs, and green nodes represent the genes down-regulated in NFPAs. Circle nodes stand for known disease genes, whereas triangle nodes stand for potential novel disease genes. Node size positively correlates with node degree, namely, the number of neighbors. PPI: protein-protein interaction; DEGs: differentially expressed genes; NFPAs: non-functioning pituitary adenomas.

The PPI sub-network containing the top 10 DEGs. Red nodes represent the genes up-regulated in NFPAs, and green nodes represent the genes down-regulated in NFPAs. Circle nodes stand for known disease genes, whereas triangle nodes stand for potential novel disease genes. Node size positively correlates with node degree, namely, the number of neighbors. PPI: protein-protein interaction; DEGs: differentially expressed genes; NFPAs: non-functioning pituitary adenomas.

The top 10 up-regulated genes and top 10 down-regulated genes.

Genes	Log₂ FC	Correctedp Value	Gene Title
Up-regulated
SSBP2	2.04	1.43E-10	single-stranded DNA binding protein 2
CDH10	2.68	1.43E-10	cadherin 10, type 2 (T2-cadedrin)
FAM171A1	2.18	2.45E-10	family with sequency similarity 171, member A1
EFNB3	2.05	8.76E-10	ephrin-B3
PCYT1B	2.16	9.13E-10	phosphate cytidylytransferase 1, choline, β
RNF157	2.26	1.16E-09	ring finger protein 157
CDK18	2.46	1.57E-09	cyclin-dependent kinase 18
LRFN5	3.63	2.01E-09	leucine rich repeat and fibronectin type III domain containing 5
CACNA2D4	4.11	2.92E-09	calcium channel, voltage-dependent, a2/δ subunit 4
P PARGC1B	2.97	5.94E-09	peroxisome proliferator-activated receptor γ, coactivator 1 β
Down-regulated
GH1	–9.74	1.49E-21	growth hormone 1
CSH1	–8.67	3.69E-15	chorionic somatomammotropin hormone 1 (placental lactogen)
DLK1	–9.33	4.16E-15	δ-like 1 homolog (Drosophila)
CSH2	–9.17	3.14E-13	chorionic somatomammotropin hormone 2
HIP1R	–2.16	5.43E-12	huntingtin interacting protein 1 related
CDKN2A	–2.33	4.74E-11	cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)
MGP	–2.86	8.06E-11	matrix Gla protein
KCNJ6	–3.79	9.50E-11	potassium inwardly-rectifying channel, subfamily J, member 6
SPRY4	–2.32	1.03E-10	sprouty homolog 4 (Drosophila)
MEG3	–5.72	1.60E-10	maternally expressed 3 (non-protein coding)

Significantly enriched terms.

Category	Term ID	Correctedp Value	Numberof DEGs	Number ofGenes	Term
KEGG	K04610	3.18E-04	10	69	complement and coagulation cascades
	K04512	3.97E-04	11	84	extracellular matrix-receptor interaction
	K04010	4.55E-03	20	271	MAPK signaling pathway
	K04115	5.32E-02	8	69	p53 signaling pathway
	K00350	6.79E-03	9	87	transforming growth factor β signaling pathway
	K04630	7.62E-03	13	155	Jak-STAT signaling pathway
	K04080	1.14E-02	18	256	neuroactive ligand-receptor interaction
	K04510	1.27E-02	15	202	focal adhesion
	K05218	2.08E-02	7	71	Melanoma
	K05412	2.90E-02	7	76	arrhythmogenic right ventricular cardiomopathy
	K05210	4.63E-02	7	84	colorectal cancer
	K04920	4.70E-02	6	67	adipocytokine signaling pathway
GO BP	GO:0032501	2.26E-24	266	4974	multicellular organismal process
(top 10)	GO:0010243	6.92E-13	57	596	response to organic nitrogen
	GO:0007275	4.19E-12	112	2080	multicellular organismal development
	GO:0048583	2.00E-10	99	1624	regulation of response to stimulus
	GO:0023051	4.23E-10	110	1866	regulation of signaling
	GO:0010646	5.12E-10	110	1872	regulation of cell communication
	GO:0048812	1.38E-09	49	571	neuron projection morphogenesis
	GO:0048667	3.03E-09	48	566	cell morphogenesis involved in neuron differentiation
	GO:0007243	3.09E-09	64	879	intracellular protein kinase cascade
	GO:0022008	6.39E-09	63	900	neurogenesis
GO CC	GO:0005576	1.31E-14	132	2164	extracellular region
(top 10)	GO:0005615	1.19-E-09	61	848	extracellular space
	GO:0005587	1.37E-05	4	6	collagen type IV
	GO:0005581	1.90E-05	12	88	collagen
	GO:0043005	5.12E-05	39	634	neuron projection
	GO:0005578	5.72E-05	18	204	proteinaceous extracellular matrix
	GO:0031012	8.74E-05	9	62	extracellular matrix
	GO:0016323	1.39E-04	15	158	basolateral plasma membrane
	GO:0005887	5.55E-04	59	1216	integral to plasma membrane
	GO:0005584	9.84E-04	2	2	collagen type I
GO MF	GO:0005201	2.40E-10	17	78	extracellular matrix structural constituent
(top 10)	GO:0008201	1.20E-07	18	129	heparin binding
	GO:0097367	1.60E-07	22	191	carbohydrate derivative binding
	GO:0042803	5.71E-06	38	553	protein homodimerization binding
	GO:0005179	9.11E-11	14	110	hormone activity
	GO:0000981	1.75E-05	22	253	sequence specific DNA binding RNA polymerase II transcription factor activity
	GO:0001077	4.36E-05	10	67	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription
	GO:0019199	5.05E-05	11	82	transmembrane receptor protein kinase activity
	GO:0005102	1.92E-04	55	1093	receptor binding
	GO:0048407	2.70E-04	4	11	platelet-derived growth factor binding

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Microarray technology reveals potentially novel genes and pathways involved in non-functioning pituitary adenomas

Article Category: Original Article

Published Online: Dec 31, 2016

Page range: 5 - 16

DOI: https://doi.org/10.1515/bjmg-2016-0030

KeywordsDifferentially expressed genes (DEGs), Functional enrichment analysis, Microarray, Non-functioning pituitary adenomas (NFPAs), Protein-protein interaction (PPI)

© 2016 Qiao X, Wang H, Wang X, Zhao B, Liu J

This article is distributed under the terms of the Creative Commons Attribution Non-Commercial License, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

The top 10 up-regulated genes and top 10 down-regulated genes.

Significantly enriched terms.

Keywords
Differentially expressed genes (DEGs), Functional enrichment analysis, Microarray, Non-functioning pituitary adenomas (NFPAs), Protein-protein interaction (PPI)