DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells

Cavalieri, Duccio; Rivero, Damariz; Beltrame, Luca; Buschow, Sonja I; Calura, Enrica; Rizzetto, Lisa; Gessani, Sandra; Gauzzi, Maria C; Reith, Walter; Baur, Andreas; Bonaiuti, Roberto; Brandizi, Marco; De Filippo, Carlotta; D'Oro, Ugo; Draghici, Sorin; Dunand-Sauthier, Isabelle; Gatti, Evelina; Granucci, Francesca; Gündel, Michaela; Kramer, Matthijs; Kuka, Mirela; Lanyi, Arpad; Melief, Cornelis JM; van Montfoort, Nadine; Ostuni, Renato; Pierre, Philippe; Popovici, Razvan; Rajnavolgyi, Eva; Schierer, Stephan; Schuler, Gerold; Soumelis, Vassili; Splendiani, Andrea; Stefanini, Irene; Torcia, Maria G; Zanoni, Ivan; Zollinger, Raphael; Figdor, Carl G; Austyn, Jonathan M

doi:10.1186/1745-7580-6-10

Immunome Research

Table 1 DC-ATLAS curation results: number and names of new genes present in TLR pathways of DC

From: DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells

TLR signaling pathways Cascade	Genes in revised pathway	New genes in revised pathway	Names of new genes or chemicals previously absent from the DCs pathway (Entrez Gene ID)
TLR1/TLR2	72	21	Transduction modules: SOCS1 (8651), BTK (695), PPARG (5468). Outcomes: CXCL2 (2920), IL2 (3558), MAP3K8 (1326), MHC (HLA-E (3133), HLA-DMB (3109), HLA-DOA (3111), HLA-DPA1 (3113), HLA-DPB1 (3115), HLA-DQA1 (3117), HLA-DQB1 (3119), HLA-DRA (3122), HLA-DRB1 (3123), HLA-DRB3 (3125), HLA-DRB4 (3126), HLA-DRB5 (3127)), CD86 (942), CCL19 (6363), CCL2 (6347).
TLR2/TLR6	78	26	Transduction modules: SOCS1 (8651), BTK (695), PPARG(5468), PRKCA (5578) Outcomes: CXCL2 (2920), IL2 (3558), MAP3K8 (1326), MHC (HLA-E (3133), HLA-DMB (3109), HLA-DOA (3111), HLA-DPA1 (3113), HLA-DPB1 (3115), HLA-DQA1 (3117), HLA-DQB1 (3119), HLA-DRA (3122), HLA-DRB1 (3123), HLA-DRB3 (3125), HLA-DRB4 (3126), HLA-DRB5 (3127)), CD86 (942), CCL19 (6363), CCL2 (6347), IL10 (3586), CD80 (941), CD40 (958), CCR7 (1236).
TLR3	66	23	Transduction modules: PRKCA (5578), PRKCB1(5579), CREBBP (1387), SRC (6714), AKT1 (207). Outcomes: IL10 (3586), IL29 (282618), IL28A(282616), IL28B (282617), IL1A (3552), CCL3 (6348), CCR7 (1236), CD274 (29126), STAT4 (6775), SOCS1 (8651), INDO (3620), ICAM1 (3383), CD83 (9308), MHC(HLA-DRB5 (3127), HLA-DRB4 (3126), HLA-DRB3 (3125), HLA-DRB1 (3123), HLA-DRA (3122)).
TLR4	100	37	Transduction modules: PI(4,5)P2, IRAK2 (3656), IRAK3 (11213), MAP3K7IP3 (257397), The protein family dynamin (DNM3 (26052), DNM2 (1785), DNM1 (1759)), RIPK3 (11035), TNKS (8658), AZI2 (64343), TBKBP1 (9755). Outcomes: IL1A (3552), IL10 (3586), IL12A (3592), IL12B (3593), IL15 (3600), IL23A (51561), LTA (4049), CCL19 (6363), TNFSF10 (8743), IRF1 (3659), IRF3 (3661), IRF5 (3663), IRF7 (3665), IRF9 (10379), CXCL10 (3627), MHC (HLA-E (3133), HLA-DMB (3109), HLA-DOA (3111), HLA-DPA1 (3113), HLA-DPB1 (3115), HLA-DQA1 (3117), HLA-DQB1 (3119), HLA-DRA (3122), HLA-DRB1 (3123), HLA-DRB3 (3125), HLA-DRB4 (3126), HLA-DRB5 (3127)).
TLR5	52	25	Transduction modules: The protein family PI3K (PIK3R2 (5296), PIK3CG (5294), PIK3CD (5293), PIK3CB (5291), PIK3CA (5290), PIK3C3 (5289), PIK3C2G (5288), PIK3C2B (5287), PIK3C2A (5286), PIK3R1 (5295), PIK3R5 (23533), PIK3R6 (146850), PIK3R4 (30849), PIK3R1OS (404543), PIK3R3 (8503)), PRKD1 (5587), AKT1 (207). Outcomes: CXCL2 (2920), IL18 (3606), CCL20 (6364), IL10 (3586), IL12A (3592), IL12B (3593), IL18 (3606), CCL2 (6347).
TLR7	56	7	Transduction modules: MEF2C (4208), PIK3CA (5290), PIK3CB (5291), PIK3CG (5294), IRF4 (3662). Outcomes: IL12A (3592), IL12B (3593).
TLR8	52	5	Transduction modules: MEF2C (4208), IRF1 (3659). Outcomes: IL12A (3592), IL12B (3593), NOS2 (4843).
TLR9	54	21	Sensing module: UNC93B1 (81622). Transduction modules: PIK3CD (5293). Outcomes: MHCII (HLA-DMB (3109), HLA-DOA (3111), HLA-DPA1 (3113), HLA-DPB1 (3115), HLA-DQA1 (3117), HLA-DQB1 (3119), HLA-DRA (3122), HLA-DRB1 (3123), HLA-DRB3 (3125), HLA-DRB4 (3126), HLA-DRB5 (3127)), CD80 (941), CD83 (9308), CD86(942), CD40(958), CCL3 (6348), CXCL10 (3627), ICAM1(3383), CCR7 (1236).

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