PDGFRA

NameSynonymsFull NameRefSeq IDDescription (.pdf)IGV-img (humangenome)Sashimi-img (humangenome)UCSC-img (humangenome)IGV-img (batgenome)
PDGFRA AY229892, NM_006206, NP_006197,CD140a, PDGFR2 platelet-derived growth factor receptor, alpha polypeptide NM_006206 pdf

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Description

Homo sapiens platelet-derived growth factor receptor, alpha polypeptide (PDGFRA) encodes a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. These growth factors are mitogens for cells of mesenchymal origin. The identity of the growth factor bound to a receptor monomer determines whether the functional receptor is a homodimer or a heterodimer, composed of both platelet-derived growth factor receptor alpha and beta polypeptides. Studies suggest that this gene plays a role in organ development, wound healing, and tumor progression. Mutations in this gene have been associated with idiopathic hypereosinophilic syndrome, somatic and familial gastrointestinal stromal tumors, and a variety of other cancers.

RPL21P44: Homo sapiens ribosomal protein L21 pseudogene 44 (RPL21P44), non-coding RNA CHIC2 (aka B2R639, BTL, CHIC2\_HUMAN, NM\_012110, NP\_036242, Q9UKJ5): his gene encodes a member of the CHIC family of proteins. The encoded protein contains a cysteine-rich hydrophobic (CHIC) motif, and is localized to vesicular structures and the plasma membrane. This gene is associated with some cases of acute myeloid leukemia. GSX2 (aka GSH2, GSX2\_HUMAN, NM\_133267, NP\_573574, Q9BZM3): Homo sapiens GS homeobox 2 (GSX2), mRNA. FIP1L1 (aka FIP1, NM\_001134938, NP\_001128410, Q6UN15-3, RHE): Homo sapiens FIP1 like 1 (S. cerevisiae) (FIP1L1), transcript variant 3 encodes a subunit of the CPSF (cleavage and polyadenylation specificity factor) complex that polyadenylates the 3' end of mRNA precursors. This gene, the homolog of yeast Fip1 (factor interacting with PAP), binds to U-rich sequences of pre-mRNA and stimulates poly(A) polymerase activity. Its N-terminus contains a PAP-binding site and its C-terminus an RNA-binding domain. An interstitial chromosomal deletion on 4q12 creates an in-frame fusion of human genes FIP1L1 and PDGFRA (platelet-derived growth factor receptor, alpha). The FIP1L1-PDGFRA fusion gene encodes a constitutively activated tyrosine kinase that joins the first 233 amino acids of FIP1L1 to the last 523 amino acids of PDGFRA. This gene fusion and chromosomal deletion is the cause of some forms of idiopathic hypereosinophilic syndrome (HES). This syndrome, recently reclassified as chronic eosinophilic leukemia (CEL), is responsive to treatment with tyrosine kinase inhibitors. Alternative splicing results in multiple transcript variants encoding distinct isoforms. LNX1 (aka LNX, LNX1\_HUMAN, NM\_001126328, NP\_001119800, PDZRN2, Q4W5K7, Q8N4C2, Q8TBB1, Q96MJ7, Q9BY20, uc003hag.4, UNQ574/PRO1136): Homo sapiens ligand of numb-protein X 1, E3 ubiquitin protein ligase (LNX1), transcript variant 1 encodes a membrane-bound protein that is involved in signal transduction and protein interactions. The encoded product is an E3 ubiquitin-protein ligase, which mediates ubiquitination and subsequent proteasomal degradation of proteins containing phosphotyrosine binding (PTB) domains. This protein may play an important role in tumorogenesis. Alternatively spliced transcript variants encoding distinct isoforms have been described. A pseudogene, which is located on chromosome 17, has been identified for this gene.

The hg19 locus of PDGFRA gene covers at the 3' end the UCSC annotated FIP1L1 gene and covers by intron an antisense located LNX1 gene (with again antisense ncRNAs LNX1-AS 1 and 2). In the last third it covers the antisense annotated RPL21P44 and CHiC2 gene. The antisense LNX1 gene is equally expressed over all samples, but shows in front of the last exon a differential expressed intron transcript: human up- (3-7h) and downregulation (7-23h), ebola down- (3-7h) and upregulation (7-23h) and up- (3-7h) and downregulation (7-23h). Onto the RPL2 and GSX2 gene no reads were mapped. In contrast the CHIC2 gene shows equal expression in human for ebola infection an upregulation and for marburg infection a downregulation. Its 3' UTR is expressed too, equal distributed over all samples. Regarding the PDGFRA gene in hg19 is down regulated in mock and ebola, but upregulated during marburg infection. Some introns are slightly expressed, like the 9th one, that shows in human the expression pattern of up- (3-7h) and downregulation (7-23h), infected with ebola 3 fold upregulation and infected with marburg a 2 fold downregulation. The homolog sequence in R.~aegyptiacus is slightly downregulated over all samples.

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Maximum read counts and DESeq normalized read counts for human and bat cell lines

Source Species Mapping on Mock3h Mock7h Mock23h EBOV3h EBOV7h EBOV23h MARV3h MARV7h MARV23h
Read_Max
humanH. sapiensGenome138 147 147 150 163 80 122 180 163
Read_Max
batR. aegyptiacusTranscriptome 374 374 248 278 240 174 251 379 298
Read_Max
bat_genomeR. aegyptiacusGenome 477 392 307 368 253 100 227 542 359
DESeq
humanH. sapiensGenome 3014.92 3616.45 4334.68 2930.27 3681.23 1495.89 2731.74 3344.68 4738.57
DESeq
batR. aegyptiacusTranscriptome 6007.16 5532.46 5859.49 5523.4 5152.3 2841.96 5774.39 5756.37 4844.26
DESeq
bat_genomeR. aegyptiacusGenome 9067.42 8300.87 8076.0 8746.14 7867.63 4337.88 8874.81 8477.39 7084.13

Human Condition Comparisons

human Mock EBOV MARV FCMock_EBOV FCMock_MARV FCEBOV_MARV
3h 3014.92 2930.27 2731.74 -0.04 -0.14 -0.1
7h 3616.45 3681.23 3344.68 0.03 -0.11 -0.14
23h 4334.68 1495.89 4738.57 -1.53 0.13 1.66

Human Time Point Comparisons

human 3h 7h 23h FC3h_7h FC3h_23h FC7h_23h
Mock 3014.92 3616.45 4334.68 0.26 0.52 0.26
Ebov 2930.27 3681.23 1495.89 0.33 -0.97 -1.3
Marv 2731.74 3344.68 4738.57 0.29 0.79 0.5

Bat Condition Comparisons

bat Mock EBOV MARV FCMock_EBOV FCMock_MARV FCEBOV_MARV
3h 6007.16 5523.4 5774.39 -0.12 -0.06 0.06
7h 5532.46 5152.3 5756.37 -0.1 0.06 0.16
23h 5859.49 2841.96 4844.26 -1.04 -0.27 0.77

Bat Time Point Comparisons

bat 3h 7h 23h FC3h_7h FC3h_23h FC7h_23h
Mock 6007.16 5532.46 5859.49 -0.12 -0.04 0.08
Ebov 5523.4 5152.3 2841.96 -0.1 -0.96 -0.86
Marv 5774.39 5756.37 4844.26 -0.0 -0.25 -0.25