perfil transcript mico y prote mico de mcf7 ccd18 y jurkat n.
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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.

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slide2

Anotación del cromosoma 16

Chromosome 16

486 HPA antibodiesfor Chr16 proteins, 121 forunknown

ENSEMBL V68

SWISSPROT V2012_06

GPMDBV102012

HPA V10.0

110 OMIM hits

Obesity

Neurodegenerativediseases

Cancer

2300 genes

870 proteincodinggenes

305 unknownproteins

Proteinexpressionvectorsfor260 Chr16 proteins, 58 unknown

Coverage of 71% gene products in

Lynphoidcells

Epitelial cells

Fibroblasts

Shotgun

Proteomic

analysis

Transcriptomic

analysis

Data integration

Gene expressionprofile

Proteinprofile

Global and celltypespecificoutcomes

Correlationproteome/transcriptome

Proteomecoverage and chromosomedistribution

Chr16 proteomecoverage

slide3

Análisis transcriptómico

GeneChip

AffymetrixHuGene 1.0 ST

RMA normalization

Filtering of low expression probes

Selection: expressionthreshold

R/Bioconductor

FACTORY

Transcriptionfactors

INGENUITY

Networks, pathways and functions

MCF7

CCD18

Jurkat

www.affymetrix.com

slide4

Cálculo del umbral de expresión génica

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.

slide5

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.

Genes que codifican proteínas no detectados en las condiciones analíticas del experimento

slide6

Shotgunproteomics. 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 (Ensv68) located in this chromosome.