{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["7091"],"full_dataset_link":["https://pax-db.org/dataset/7091/1004366984"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["Bombyx mori cocoon has a multi-layer structure that provides optimal protection for silkworm pupa. Research on the mechanical properties of the multi-layer structure revealed structure-property relationships of the cocoon. Here, we investigated the protein components of the B. mori cocoon in terms of its multi-layer structure. Liquid chromatography-tandem mass spectrometry identified 286 proteins from the multiple cocoon layers. In addition to fibroins and sericins, we identified abundant protease inhibitors, seroins and proteins of unknown function. By comparing protein abundance across layers, we found that the outermost layer contained more sericin1 and protease inhibitors and the innermost layer had more seroin1. As many as 36 protease inhibitors were identified in cocoons, showing efficient inhibitory activities against a fungal protease. Thus, we propose that more abundant protease inhibitors in the outer cocoon layers may provide better protection for the cocoon. This study increases our understanding of the multi-layer mechanism of cocoons, and helps clarify the biological characteristics of cocoons. The data have been deposited to the ProteomeXchange with identifier PXD001469."],"pubmed_title":["Comparative proteome analysis of multi-layer cocoon of the silkworm, Bombyx mori."],"pubmed_authors":["Zhang Yan Y, Zhao Ping P, Dong Zhaoming Z, Wang Dandan D, Guo Pengchao P, Guo Xiaomeng X, Song Qianru Q, Zhang Weiwei W, Xia Qingyou Q"],"citation_count":["0"],"additional_accession":[]},"is_claimable":false,"name":"Bmori - Cocoon, SC (Zhangetal.,plosone2015)","description":"abundance based on Spectral counting, Interaction consistency score: 1.0, Coverage: 2","dates":{"publication":"2015"},"accession":"1004366984","cross_references":{"pubmed":["25860555"],"uniprot":["H9J4M4_BOMMO","H9JBP6_BOMMO","H9JC16_BOMMO","H9IZF9_BOMMO","H9IS19_BOMMO","H9JTP8_BOMMO","E5EVW3_BOMMO","LYS_BOMMO","H9IV93_BOMMO","H9JMY9_BOMMO","H9J9P2_BOMMO","H9JN76_BOMMO","H9JTC5_BOMMO","H9IVS9_BOMMO","H9IZI1_BOMMO","H9IVT6_BOMMO","H9JUB6_BOMMO","H9JFR3_BOMMO","VIT_BOMMO","H9JHA7_BOMMO","Q2F5Q6_BOMMO","H9IZL9_BOMMO","H9JYA0_BOMMO","H9JRS9_BOMMO","H9JBL0_BOMMO","H9J011_BOMMO","H9JH31_BOMMO","SSP2_BOMMO","H9JGX1_BOMMO","H9JU99_BOMMO","H9IZ88_BOMMO","H9JAH3_BOMMO","H9IX15_BOMMO","SI25_BOMMO","Q6T3A7_BOMMO","H9J585_BOMMO","H9JYF4_BOMMO","Q9XXZ4_BOMMO","H9JK23_BOMMO","O01953_BOMMO","C7EPE2_BOMMO","H9JQH2_BOMMO","H9J4L6_BOMMO","H9J303_BOMMO","H9J453_BOMMO","H9J4K5_BOMMO","H9JRT0_BOMMO","H9J0R5_BOMMO","B9VJ79_BOMMO","H9J5L5_BOMMO","H9IWF3_BOMMO","H9J3H2_BOMMO","H9IYU4_BOMMO","H9JK97_BOMMO","L301_BOMMO","H9J8B3_BOMMO","H9J8I8_BOMMO","H9IWI8_BOMMO","H9J4L7_BOMMO","H9JWN7_BOMMO","H9JIB1_BOMMO","H9JHM9_BOMMO","H9IYF4_BOMMO","H9J2F1_BOMMO","H9JUB7_BOMMO","TCTP_BOMMO","H9J5S9_BOMMO","H9JPG9_BOMMO","H9J593_BOMMO","IDGFL_BOMMO","H9IZI5_BOMMO","H9JL76_BOMMO","H9ISJ8_BOMMO","H9JA73_BOMMO","H9JWW6_BOMMO","Q1HPY5_BOMMO","BGBP_BOMMO","H9J5S6_BOMMO","H9JP90_BOMMO","H9ISI0_BOMMO","H9J243_BOMMO","H9IUA7_BOMMO","H9J1X1_BOMMO","H9ITL0_BOMMO","H9J868_BOMMO","H9JX84_BOMMO","H9JDF0_BOMMO","CALR_BOMMO","H9JHS4_BOMMO","H9JIA9_BOMMO","H9JDX3_BOMMO","B0ZT34_BOMMO","PRP2_BOMMO","H9J850_BOMMO","H9JQ96_BOMMO","Q1EPM0_BOMMO","H9IWH9_BOMMO","H9JQN8_BOMMO","H9JTT6_BOMMO","H9JPS6_BOMMO","Q1HPY3_BOMMO","H9JY09_BOMMO","H9JBZ7_BOMMO","H9IVR7_BOMMO","H9J8I6_BOMMO","H9JXK3_BOMMO","H9JJV0_BOMMO","H9JUB8_BOMMO","H9J6I9_BOMMO","H9JCK9_BOMMO","Q9BPS3_BOMMO","H9JUK2_BOMMO","H9J8J0_BOMMO","H9JIY7_BOMMO","H9JKT2_BOMMO","H9J8I5_BOMMO","H9J3A7_BOMMO","H9JGT9_BOMMO","H9JLM2_BOMMO","H9J9T8_BOMMO","H9J1D9_BOMMO","Q2F644_BOMMO","Q402D9_BOMMO","H9JYA3_BOMMO","H9JXF8_BOMMO","H9J4G1_BOMMO","H9J9W8_BOMMO","H9JXD8_BOMMO","H9J730_BOMMO","H9JBC0_BOMMO","H9IWJ7_BOMMO","H9JEA5_BOMMO","H9JD77_BOMMO","H9JDQ2_BOMMO","H9JN73_BOMMO","H9JAS8_BOMMO","P27K_BOMMO","JHBP_BOMMO","LP1_BOMMO","H9JNF6_BOMMO","A1AT_BOMMO","H9IVN9_BOMMO","H9JHU5_BOMMO","H9J5D7_BOMMO","H9JXY6_BOMMO","H9J894_BOMMO","H9JK41_BOMMO","H9IWX2_BOMMO","C0H6R2_BOMMO","H9IZK4_BOMMO","H9JKL1_BOMMO","H9JVX1_BOMMO","H9JP22_BOMMO","H9J4M7_BOMMO","H9J9Q8_BOMMO","FIBL_BOMMO","H9JK39_BOMMO","H9JQ40_BOMMO","SODC_BOMMO","H9JFH1_BOMMO","H9J7X3_BOMMO","H9J709_BOMMO","H9ITR7_BOMMO","H9JFA8_BOMMO","H9IVS7_BOMMO","Q69FX2_BOMMO","H9IWH6_BOMMO","H9JN98_BOMMO","H9JBW7_BOMMO","H9JWD5_BOMMO","H9IZI4_BOMMO","H9JTZ5_BOMMO","H9J250_BOMMO","H9IU44_BOMMO","SGF1_BOMMO","H9JBZ4_BOMMO","ACH1_BOMMO","H9J9I7_BOMMO","H9J7K1_BOMMO","H9J7R4_BOMMO","H9JW43_BOMMO","H9J1X0_BOMMO","H9J1D5_BOMMO","E9JEH5_BOMMO","H9ISA2_BOMMO","PYM_BOMMO","H9JT78_BOMMO","H9IZ19_BOMMO","H9J8H0_BOMMO","H9JLC2_BOMMO","H9JSY6_BOMMO","H9JPE5_BOMMO","H9JMS7_BOMMO","H9JYA2_BOMMO","LP2_BOMMO","H9JCC5_BOMMO","H9JCP0_BOMMO","H9IVS0_BOMMO","H9IX10_BOMMO","H9JH50_BOMMO","H9J5L9_BOMMO","Q1HPY8_BOMMO","Q6T9Z7_BOMMO","FIBH_BOMMO","H9JGY3_BOMMO","H9ISA5_BOMMO","Q5R1P5_BOMMO","SSP1_BOMMO","H9JK98_BOMMO","H9JR42_BOMMO","H9ISR3_BOMMO","E5EVW2_BOMMO","H9J012_BOMMO","H9IYR4_BOMMO","H9JR22_BOMMO","H9J9P6_BOMMO","Q2PQU4_BOMMO","G8GBC4_BOMMO","Q6Q2D6_BOMMO","H9JVK2_BOMMO","H9J168_BOMMO","H9JQU5_BOMMO","Q3LB95_BOMMO","H9JHU4_BOMMO","H9JCD8_BOMMO","H9J885_BOMMO","H9JXB3_BOMMO","H9JTY2_BOMMO","H9JAZ9_BOMMO","H9JDG1_BOMMO","H9J5D8_BOMMO","H9JMQ8_BOMMO","H9JMY8_BOMMO","H9JYJ8_BOMMO","H9JHU3_BOMMO","H9JXQ6_BOMMO","Q2F605_BOMMO","H9JDV4_BOMMO","H9IS38_BOMMO","H9J1A5_BOMMO","H9JX51_BOMMO","H9JC27_BOMMO","H9JB50_BOMMO","EF2_BOMMO","H9JU96_BOMMO","H9J6U8_BOMMO","H9B457_BOMMO","H9J502_BOMMO","H9J4G2_BOMMO","B0FPE7_BOMMO","H9JI11_BOMMO","H9J4V7_BOMMO"]}}