perfil transcriptómico y proteómico de mcf7, ccd18 y jurkat
DESCRIPTION
Perfil transcriptómico y proteómico de MCF7, CCD18 y Jurkat . Anotación del cromosoma 16. Chromosome 16. 486 HPA antibodies for Chr16 proteins , 121 for unknown. ENSEMBL V68 SWISSPROT V2012_06 GPMDBV102012 HPA V10.0. 110 OMIM hits Obesity Neurodegenerative diseases Cancer. - PowerPoint PPT PresentationTRANSCRIPT
Perfil transcriptómico y proteómico de MCF7, CCD18 y Jurkat.
Chromosome 16
ENSEMBL V68SWISSPROT V2012_06
GPMDBV102012HPA V10.0
2300 genes870 protein coding genes305 unknown proteins
110 OMIM hitsObesityNeurodegenerative diseasesCancer
Coverage of 71% gene products inLynphoid cellsEpitelial cellsFibroblasts Shotgun
Proteomic analysis
Transcriptomicanalysis
486 HPA antibodies for Chr16 proteins, 121 for unknown
Protein profile Gene expression profileData integration
Global and cell type specific outcomesCorrelation proteome/transcriptomeProteome coverage and chromosome distributionChr16 proteome coverage
Protein expression vectors for 260 Chr16 proteins, 58 unknown
Anotación del cromosoma 16
GeneChip Affymetrix HuGene 1.0 ST
RMA normalizationFiltering of low expression probes
Selection: expression thresholdR/Bioconductor
INGENUITY
FACTORY
Networks, pathways and functions
Transcription factors
Análisis transcriptómico
www.affymetrix.com
MCF7CCD18Jurkat
Upon data normalization, an expression threshold was calculated to eliminate low intensity probe sets that are considered technical noise. FDR values > 95% were discarded meaning that 80% of the probe sets were considered for further analyses.
Cálculo del umbral de expresión génica
Genes que codifican proteínas no detectados en las condiciones analíticas del experimento
Resumen de los resultados de expresión génica
• A total of 19340 genes were expressed in at least one of the three cell lines, 82% were common, 1% were specifically detected in MCF7 cells, 2.6% in CCD18 and 0.9% in Jurkat cells.
• Up to 1533 genes from Chr16 were not detected, most of them being non protein coding genes.
Shotgun proteomics. Resumen de resultados
• Assuming a FDR below 1% at the protein level, 9488 proteins were identified; 6092 proteins were identified in MCF7, 5547 in CCD18 and 7197 in Jurkat cells; among them, 40% were commonly found in the three cell lines.
• Among the identified proteins, 388 are encoded by Chr16 genes, representing a 44,6% of the 870 protein coding genes (Ens v68) located in this chromosome.
Distribución cromosómica de los genes y proteínas
Comparación transcriptómica/proteómica
Chr Name Description MCF7Prot MCF7Exp CCD18Prot CCD18Exp JurkatProt JurkatExp
16 PDF peptide deformylase (mitochondrial) [Source:HGNC Symbol;Acc:30012] 1 0 1 0 1 0
16 NOMO2 NODAL modulator 2 [Source:HGNC Symbol;Acc:22652] 1 0 1 0 1 0
16 IST1 increased sodium tolerance 1 homolog (yeast) [Source:HGNC Symbol;Acc:28977] 1 0 1 0 1 0
16 EMC8 COX4 neighbor [Source:HGNC Symbol;Acc:7864] 1 0 1 0 1 0
16 BOLA2B bolA homolog 2B (E. coli) [Source:HGNC Symbol;Acc:32479] 1 0 1 0 1 0
16 WASH4P WAS protein family homolog 4 pseudogene [Source:HGNC Symbol;Acc:14126] 1 0 1 0 1 0
16 DYNLRB2 dynein, light chain, roadblock-type 2 [Source:HGNC Symbol;Acc:15467] 1 0 1 0 1 0
16 HBA2 hemoglobin, alpha 2 [Source:HGNC Symbol;Acc:4824] 1 0 1 0 1 0
16 NOMO1 NODAL modulator 1 [Source:HGNC Symbol;Acc:30060] 1 0 1 0 1 0
16 RMI2RMI2, RecQ mediated genome instability 2, homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:28349] 1 0 0 0 1 0
16 PABPN1L poly(A) binding protein, nuclear 1-like (cytoplasmic) [Source:HGNC Symbol;Acc:37237] 1 0 0 0 1 0
16 CMC2 chromosome 16 open reading frame 61 [Source:HGNC Symbol;Acc:24447] 1 0 0 0 1 0
16 TSR3 chromosome 16 open reading frame 42 [Source:HGNC Symbol;Acc:14175] 0 0 0 0 1 0
16 CCP110 centriolar coiled coil protein 110kDa [Source:HGNC Symbol;Acc:24342] 0 0 0 0 1 0
16 KAT8 K(lysine) acetyltransferase 8 [Source:HGNC Symbol;Acc:17933] 0 0 0 0 1 0
16 DNAAF1 dynein, axonemal, assembly factor 1 [Source:HGNC Symbol;Acc:30539] 0 0 1 0 0 0
16 CTD-2144E22.5 0 0 1 0 0 0
16 CNEP1R1 transmembrane protein 188 [Source:HGNC Symbol;Acc:26759] 0 0 1 0 0 0
16 AC026458.2 1 0 0 0 0 0
16 ECI1 enoyl-CoA delta isomerase 1 [Source:HGNC Symbol;Acc:2703] 1 0 0 0 0 0
16 ATXN1L ataxin 1-like [Source:HGNC Symbol;Acc:33279] 1 0 0 0 0 0
16 PIEZO1 piezo-type mechanosensitive ion channel component 1 [Source:HGNC Symbol;Acc:28993] 1 0 0 0 0 0
16 SULT1A4sulfotransferase family, cytosolic, 1A, phenol-preferring, member 4 [Source:HGNC Symbol;Acc:30004] 1 0 0 0 0 0
