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

X Qiao

X Qiao

Department of Gastrointestinal Surgery, The Second Hospital of Jilin UniversityChangchun, China
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Qiao, X
, 
H Wang

H Wang

Department of Neurosurgery, The Second Hospital of Jilin UniversityChangchun, China
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Wang, H
, 
X Wang

X Wang

Department of Neurosurgery, The Second Hospital of Jilin UniversityChangchun, China
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Wang, X
, 
B Zhao

B Zhao

Department of Neurosurgery, The Second Hospital of Jilin UniversityChangchun, China
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Zhao, B
 und 
J Liu

J Liu

Department of Neurosurgery, The Second Hospital of Jilin UniversityChangchun, China
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Liu, J
  
31. Dez. 2016
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Artikel-Kategorie: Original Article
Online veröffentlicht: 31. Dez. 2016
Seitenbereich: 5 - 16
DOI: https://doi.org/10.1515/bjmg-2016-0030
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© 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).
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 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 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.
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.
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 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 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_

GenesLog2 FCCorrectedp ValueGene Title
Up-regulated
 SSBP22.041.43E-10single-stranded DNA binding protein 2
 CDH102.681.43E-10cadherin 10, type 2 (T2-cadedrin)
 FAM171A12.182.45E-10family with sequency similarity 171, member A1
 EFNB32.058.76E-10ephrin-B3
 PCYT1B2.169.13E-10phosphate cytidylytransferase 1, choline, β
 RNF1572.261.16E-09ring finger protein 157
 CDK182.461.57E-09cyclin-dependent kinase 18
 LRFN53.632.01E-09leucine rich repeat and fibronectin type III domain containing 5
 CACNA2D44.112.92E-09calcium channel, voltage-dependent, a2/δ subunit 4
 P PARGC1B2.975.94E-09peroxisome proliferator-activated receptor γ, coactivator 1 β
Down-regulated
 GH1–9.741.49E-21growth hormone 1
 CSH1–8.673.69E-15chorionic somatomammotropin hormone 1 (placental lactogen)
 DLK1–9.334.16E-15δ-like 1 homolog (Drosophila)
 CSH2–9.173.14E-13chorionic somatomammotropin hormone 2
 HIP1R–2.165.43E-12huntingtin interacting protein 1 related
 CDKN2A–2.334.74E-11cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)
 MGP–2.868.06E-11matrix Gla protein
 KCNJ6–3.799.50E-11potassium inwardly-rectifying channel, subfamily J, member 6
 SPRY4–2.321.03E-10sprouty homolog 4 (Drosophila)
 MEG3–5.721.60E-10maternally expressed 3 (non-protein coding)

Significantly enriched terms_

CategoryTerm IDCorrectedp ValueNumberof DEGsNumber ofGenesTerm
KEGGK046103.18E-041069complement and coagulation cascades
K045123.97E-041184extracellular matrix-receptor interaction
K040104.55E-0320271MAPK signaling pathway
K041155.32E-02869p53 signaling pathway
K003506.79E-03987transforming growth factor β signaling pathway
K046307.62E-0313155Jak-STAT signaling pathway
K040801.14E-0218256neuroactive ligand-receptor interaction
K045101.27E-0215202focal adhesion
K052182.08E-02771Melanoma
K054122.90E-02776arrhythmogenic right ventricular cardiomopathy
K052104.63E-02784colorectal cancer
K049204.70E-02667adipocytokine signaling pathway
GO BPGO:00325012.26E-242664974multicellular organismal process
(top 10)GO:00102436.92E-1357596response to organic nitrogen
GO:00072754.19E-121122080multicellular organismal development
GO:00485832.00E-10991624regulation of response to stimulus
GO:00230514.23E-101101866regulation of signaling
GO:00106465.12E-101101872regulation of cell communication
GO:00488121.38E-0949571neuron projection morphogenesis
GO:00486673.03E-0948566cell morphogenesis involved in neuron differentiation
GO:00072433.09E-0964879intracellular protein kinase cascade
GO:00220086.39E-0963900neurogenesis
GO CCGO:00055761.31E-141322164extracellular region
(top 10)GO:00056151.19-E-0961848extracellular space
GO:00055871.37E-0546collagen type IV
GO:00055811.90E-051288collagen
GO:00430055.12E-0539634neuron projection
GO:00055785.72E-0518204proteinaceous extracellular matrix
GO:00310128.74E-05962extracellular matrix
GO:00163231.39E-0415158basolateral plasma membrane
GO:00058875.55E-04591216integral to plasma membrane
GO:00055849.84E-0422collagen type I
GO MFGO:00052012.40E-101778extracellular matrix structural constituent
(top 10)GO:00082011.20E-0718129heparin binding
GO:00973671.60E-0722191carbohydrate derivative binding
GO:00428035.71E-0638553protein homodimerization binding
GO:00051799.11E-1114110hormone activity
GO:00009811.75E-0522253sequence specific DNA binding RNA polymerase II transcription factor activity
GO:00010774.36E-051067RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription
GO:00191995.05E-051182transmembrane receptor protein kinase activity
GO:00051021.92E-04551093receptor binding
GO:00484072.70E-04411platelet-derived growth factor binding
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