PMC

Gene Ontology classification of the proteins within the mouse secretome.

Size distribution of the proteins predicted to contain endoplasmic reticulum signal peptides within the PROCREST predicted ORFs of the RIKEN 60,770 FANTOM2 cDNA clone set and the mouse secretome. The total numbers of proteins within 50 amino acid blocks are plotted.

Distribution of InterPro domains and SCOP superfamilies associated with the mouse secretome. The proportion of individual InterPro domains (A) or SCOP superfamilies (B) within the mouse secretome relative to the total number of predicted domains within the RPS is plotted as a percentage ratio (Secretome/RPS). One hundred percent represents a domain that is only contained in proteins within the mouse secretome. All RPS protein sequences that could not be classified by the membrane organization methods were excluded ().

Hierarchical clustering of gene expression data for 970 FANTOM2 cDNAs encoding secretome proteins across 22 mouse tissues. Results are presented in a dendrogram displaying related groups of genes (on the Y-axis) and tissues (on the X-axis). The relative expression of each cDNA is represented as a log₂ ratio of hybridization signals between each tissue and a common reference mRNA sample (total 17.5 dpc mouse embryo). Blocks of red signal indicate high levels of expression in the tissue relative to the reference RNA. Blocks of green signify low levels of expression relative to the reference RNA. Grey blocks indicate data points that are missing. Along the right-hand side of the dendrogram are several yellow boxes labeled A to D, which define the location of four tissue-restricted clusters. (A) Neural restricted cluster. (B) Placenta cluster. (C) Digestive tract cluster. (D) Testis cluster.

Classification of domain architecture in CUB domain-containing proteins. (A) Graphic depiction of domain organization of the CUB-containing proteins. The 33 proteins analyzed include PC23894, hypothetical CUB-serine protease family (S1)-containing protein; PC15512, hypothetical Sushi domain-containing protein; PC12522, hypothetical Speract receptor (Scavenger receptor), CUB domain-containing protein; PB7569, Cegp1 protein; PB8024, signal peptide, CUB domain, EGF-like 1; PA1005, bone morphogenetic protein 1; PB5671, tolloid-like; PB6268, tolloid-like 2; PB6857, complement component 1, r subcomponent; PA3595, complement-activating component of ra-reactive factor; PC39138, hypothetical EGF-CUB-Sushi-Serine protease domain-containing protein; PC38939, similar to complement component 1, s subcomponent; PC40559, similar to complement component 1, s subcomponent; PB3596, mannan-binding lectin serine protease 2; PA5693, tumor necrosis factor-inducible protein tsg-6; PA4207, procollagen c-proteinase enhancer protein (PCPE); PC16805, procollagen c-terminal proteinase enhancer protein 2; PC12829, platelet-derived growth factor-C; PB7152, platelet-derived growth factor-D, PC31766, hypothetical CUB domain-containing protein; PA4026, Neuropilin-1; PA4027, Neuropilin-2; PB19077, kringle-coding gene; PB1500, crp-ductin; PC21298, hypothetical LDLRA-CUB domain-containing protein; PB8052, low-density lipoprotein receptor-related protein 10; PB19224, CUB and Sushi multiple domains 1; PC24046, similar to type I transmembrane receptor (seizure-related protein); PB5075, seizure-related gene 6; PB8627, RIKEN cDNA 4631413K11; PC12799, hypothetical serine protease, trypsin family-containing protein; PA4536, suppressor of tumorigenicity 14; PC15176, hypothetical LDLRA-CUB domain-containing protein. (B) Key for InterPro domains.