The Liverbase integrates information on the human liver proteome/ transcriptome, including the function, abundance, and subcellular localization of proteins as well as associated disease information. The overall objective of the Liverbase is to provide a unique public resource for the liver community by providing comprehensive functional annotation of proteins implicated in liver development and disease. The central database features are manually annotated proteins localized in or functionally associated with human liver.

  In this first version of Liverbase, the associated data includes the human liver proteome (6788 proteins) and transcriptome (11205 significantly expressed genes: 10224 from CHIP and 5422 from MPSS, respectively) from the Chinese human liver proteome project (CNHLPP). Table 1 provides an overview of the current data of Liverbase.

  The proteome and transcriptome expression profiling data listed in Liverbase was from the same sample. And the sample collection procedure followed the regulations of the ethics committee of the Chinese Human Liver Proteome Project. Human liver samples were collected from volunteers of the Chinese Han nationality, who had undergone hepatic hemangioma resection (neoplastic lesions were less than 5cm in diameter). Volunteers were selected from a large pool of patients. Qualified donors were free from viral hepatitis, autoimmune liver disease, cystic liver disease, fatty liver disease, and other forms of liver disease. Before surgery the donors gave informed consent and received systematic examinations, including biochemical (alanine aminotransferase, aspartate aminotransferase, g-glutamyl transferase, alkaline phosphatase, bilirubin, albumin, prothrombin time, and alpha-fetoprotein) and liver imaging (B-type ultrasound) examinations. Surgical samples were processed for proteomic analysis only if the volunteer's diagnostic data was within normal range.

  In human liver proteome, a qualified protein must satisfy the following criteria: 1) all peptide data should meet a 95% confidence cut-off; 2) false-positive matching of peptides should be eliminated after searching of the reversed IPI database; 3) for shotgun sequencing, the qualified peptide should have an MS/MS sequence of more than six amino acids. All identified proteins should have two or more peptides matches; 4) for peptide mass fingerprinting (PMF), a protein should have at least five peptide matches with 20-ppm mass tolerance in database searching.

  The pooled RNA sample from ten human-liver RNAs in same amount were labeled and hybridized to HG-U133plus 2.0 high-density oligonucleotide arrays (Affymetrix), which contains 54,675 probe sets representing 19,164 human genes and 15,136 ESTs on a single array.1μg of poly (A)+ RNA was annealed to oligo (dT) and transcribed using SurperScript II reverse transcriptase (Invitrogen, Carlsbad, CA), Labeling, hybridization, washing and signal scan on the microarrays were performed according to the manufacturer's instructions. Primary image analysis of the arrays was performed by using GENECHIP 3.2 (Affymetrix, Santa Clara, CA), and normalization was performed using Mas 5.0 software (Affymetrix). Only those transcripts that were declared “present” and more than 100 intensity of fluorescence were taken into account. To assign a signal for a gene in human liver, we selected the maximum normalized expression signal of all probe sets matched to the gene if there are multiple probe sets for a gene.

  SCIN means normalized spectral count indexes. In human liver proteome, SCIN was assigned to estimate the protein abundance from 7 large-scale batches of non-gel technology lines. Expectation maximization (EM) algorithm was performed to distribute spectral count (SC) values among identified proteins and form a spectral count indexes (SCI). SCI values in each batch were normalized, and the final semiquantitation indexes were constructed by arithmetic means of each identified protein.

   If you use Liverbase in any published work, please cite the following reference: Sun, A.; Jiang, Y.; Wang, X.; Liu, Q.; Zhong, F.; He, Q.; Guan, W.; Li, H.; Sun, Y.; Shi, L.; Yu, H.; Yang, D.; Xu, Y.; Song, Y.; Tong, W.; Li, D.; Lin, C. L.; Hao, Y.; Geng, C.; Yun, D.; Zhang, X.; Yuan, X.; Chen, P.; Zhu, Y.; Li, Y.; Liang, S.; Zhao, X. H.; Liu, S.; He, F., Liverbase: a comprehensive view of human liver biology. J Proteome Res 2009.

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