Table 4.
Hub genes identified in the tubulointerstitial PIN
| Rank | Gene symbol | Full name | Description | Degrees |
|---|---|---|---|---|
| 1 | EGFR | Epidermal growth factor receptor | The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor. Binding of the protein to a ligand induces receptor dimerization and tyrosine autophosphorylation and leads to cell proliferation | 99 |
| 2 | LMNA | Lamin A/C | The nuclear lamina consists of a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Alternative splicing results in multiple transcript variants. Mutations in this gene lead to several diseases: Emery–Dreifuss muscular dystrophy, familial partial lipodystrophy, limb–girdle muscular dystrophy, dilated cardiomyopathy, Charcot–Marie–Tooth disease and Hutchinson–Gilford progeria syndrome | 48 |
| 3 | NRAS | NRAS proto-oncogene, GTPase | This is an N-ras oncogene encoding a membrane protein that shuttles between the Golgi apparatus and the plasma membrane. This shuttling is regulated through palmitoylation and depalmitoylation by the ZDHHC9-GOLGA7 complex. The encoded protein, which has intrinsic GTPase activity, is activated by a guanine nucleotide-exchange factor and inactivated by a GTPase activating protein. Mutations in this gene have been associated with somatic rectal cancer, follicular thyroid cancer, autoimmune lymphoproliferative syndrome, Noonan syndrome and juvenile myelomonocytic leukemia | 47 |
| 4 | HSPD1 | Heat shock protein family D (Hsp60) member 1 | This gene encodes a member of the chaperonin family. The encoded mitochondrial protein may function as a signaling molecule in the innate immune system. This protein is essential for the folding and assembly of newly imported proteins in the mitochondria. This gene is adjacent to a related family member and the region between the two genes functions as a bidirectional promoter. Several pseudogenes have been associated with this gene. Two transcript variants encoding the same protein have been identified for this gene. Mutations associated with this gene cause autosomal recessive spastic paraplegia 13 | 46 |
| 5 | HEXIM1 | HEXIM P-TEFb complex subunit 1 | Expression of this gene is induced by hexamethylene-bis-acetamide in vascular smooth muscle cells | 43 |
| 6 | TGOLN2 | Trans-golgi network protein 2 | This gene encodes a type I integral membrane protein that is localized to the trans-Golgi network, a major sorting station for secretory and membrane proteins. The encoded protein cycles between early endosomes and the trans-Golgi network and may play a role in exocytic vesicle formation | 42 |
| 7 | MAPK6 | Mitogen-activated protein kinase 6 | The protein encoded by this gene is a member of the Ser/Thr protein kinase family and is most closely related to MAP kinases. MAP kinases also known as extracellular signal-regulated kinases, are activated through protein phosphorylation cascades and act as integration points for multiple biochemical signals. This kinase is localized in the nucleus and has been reported to be activated in fibroblasts upon treatment with serum or phorbol esters | 40 |
| 8 | RC3H2 | Ring finger and C-x8-C-x5-C-x3-H (CCCH)-type domains 2 | RC3H2 is a protein coding gene. GO annotations related to this gene include mRNA binding | 36 |
| 9 | CHD3 | Chromodomain helicase DNA binding protein 3 | This gene encodes a member of the CHD family of proteins which are characterized by the presence of chromo (chromatin organization modifier) domains and SNF2-related helicase/ATPase domains. This protein is one of the components of a histone deacetylase complex referred to as the Mi-2/nucleosome remodeling and deacetylase(NuRD) complex which participates in the remodeling of chromatin by deacetylating histones. Chromatin remodeling is essential for many processes including transcription. Autoantibodies against this protein are found in a subset of patients with dermatomyositis | 35 |
| 10 | SUZ12 | SUZ12 polycomb repressive complex 2 subunit | This zinc finger gene has been identified at the breakpoints of a recurrent chromosomal translocation reported in endometrial stromal sarcoma. Recombination of these breakpoints results in the fusion of this gene and juxtaposed with another zinc finger protein 1 (JAZF1) | 34 |
Descriptions of the genes were abstracted from the RefSeq database. As no summary was available for RC3H2 in Refseq, the GeneCards summary was used instead.