Make a table with ligands and receptors in R with OmnipathR

2020-11-24

Curated lists of genes help computational biologists to focus analyses on a subset of genes that might be important for a research question. For example, we might be interested to focus on the genes encoding the signals and receptors for cell-to-cell communication. OmnipathR is a new R package that provides access to a vast database of genes called OmniPath, organized and curated by the Saez-Rodriguez Lab. Let's try to use OmnipathR to create a simple table with ligands and receptors.

Install OmnipathR#

Let's get the latest development version from GitHub. For me, that was 1.3.7 when I wrote this post.

devtools::install_github("saezlab/OmnipathR")

Make a table of ligands and receptors#

Load the package.

library(OmnipathR)
library(dplyr)

OmniPath has a lot of annotations and functions for accessing them.

Let's try the import_intercell_network() function.

icn <- OmnipathR::import_intercell_network()

The returned icn object is a data frame with 30,265 rows and 44 columns. It's a lot of information!

Download the table#

Download the entire table with 30,265 rows:

💾 omnipath-intercell-network.tsv (12.2 Mb)

Explore the first 100 records#

Lets have a look at the first 100 records:

category_intercell_source parent_intercell_source source target category_intercell_target parent_intercell_target target_genesymbol source_genesymbol is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition dip_url sources references curation_effort n_references n_resources database_intercell_source scope_intercell_source aspect_intercell_source category_source_intercell_source genesymbol_intercell_source entity_type_intercell_source consensus_score_intercell_source transmitter_intercell_source receiver_intercell_source secreted_intercell_source plasma_membrane_transmembrane_intercell_source plasma_membrane_peripheral_intercell_source database_intercell_target scope_intercell_target aspect_intercell_target category_source_intercell_target genesymbol_intercell_target entity_type_intercell_target consensus_score_intercell_target transmitter_intercell_target receiver_intercell_target secreted_intercell_target plasma_membrane_transmembrane_intercell_target plasma_membrane_peripheral_intercell_target
adhesion adhesion A4D0S4 O75578 adhesion adhesion ITGA10 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGA10 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 O75578 matrix_adhesion matrix_adhesion ITGA10 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA10 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 O75578 receptor receptor ITGA10 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;CellPhoneDB;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA10 protein 8 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P05106 adhesion adhesion ITGB3 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGB3 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P05106 matrix_adhesion matrix_adhesion ITGB3 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB3 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P05106 receptor receptor ITGB3 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;Baccin2019;OmniPath generic functional resource_specific ITGB3 protein 11 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P05556 adhesion adhesion ITGB1 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGB1 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P05556 matrix_adhesion matrix_adhesion ITGB1 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB1 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P05556 receptor receptor ITGB1 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;ICELLNET;Surfaceome;Ramilowski2015;Kirouac2010;LRdb;Baccin2019;OmniPath generic functional resource_specific ITGB1 protein 13 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P06756 adhesion adhesion ITGAV LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGAV protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P06756 matrix_adhesion matrix_adhesion ITGAV LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGAV protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P06756 receptor receptor ITGAV LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;ICELLNET;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGAV protein 11 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P08514 adhesion adhesion ITGA2B LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite ITGA2B protein 1 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P08514 matrix_adhesion matrix_adhesion ITGA2B LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA2B protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P08514 receptor receptor ITGA2B LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA2B protein 10 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P08648 adhesion adhesion ITGA5 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGA5 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P08648 matrix_adhesion matrix_adhesion ITGA5 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA5 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P08648 receptor receptor ITGA5 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA5 protein 10 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P13612 adhesion adhesion ITGA4 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE MCAM;Adhesome;OmniPath generic functional resource_specific ITGA4 protein 3 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P13612 matrix_adhesion matrix_adhesion ITGA4 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA4 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P13612 receptor receptor ITGA4 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA4 protein 9 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P16070 adhesion adhesion CD44 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite CD44 protein 1 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion A4D0S4 P16070 cell_adhesion cell_adhesion CD44 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite CD44 protein 0 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion A4D0S4 P16070 matrix_adhesion matrix_adhesion CD44 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific CD44 protein 1 FALSE TRUE TRUE TRUE FALSE
adhesion adhesion A4D0S4 P16070 receptor receptor CD44 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;ICELLNET;Ramilowski2015;LRdb;Baccin2019;OmniPath generic functional resource_specific CD44 protein 10 FALSE TRUE TRUE TRUE FALSE
adhesion adhesion A4D0S4 P17301 adhesion adhesion ITGA2 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGA2 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P17301 matrix_adhesion matrix_adhesion ITGA2 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA2 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P17301 receptor receptor ITGA2 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA2 protein 9 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P18084 adhesion adhesion ITGB5 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGB5 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P18084 matrix_adhesion matrix_adhesion ITGB5 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB5 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P18084 receptor receptor ITGB5 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGB5 protein 9 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P18564 adhesion adhesion ITGB6 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGB6 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P18564 matrix_adhesion matrix_adhesion ITGB6 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB6 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P18564 receptor receptor ITGB6 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGB6 protein 9 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26006 adhesion adhesion ITGA3 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGA3 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26006 matrix_adhesion matrix_adhesion ITGA3 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA3 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26006 receptor receptor ITGA3 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA3 protein 10 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26010 adhesion adhesion ITGB7 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGB7 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26010 cell_adhesion cell_adhesion ITGB7 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite ITGB7 protein 0 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26010 matrix_adhesion matrix_adhesion ITGB7 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB7 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26010 receptor receptor ITGB7 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGB7 protein 10 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26012 adhesion adhesion ITGB8 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGB8 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26012 matrix_adhesion matrix_adhesion ITGB8 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB8 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P26012 receptor receptor ITGB8 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGB8 protein 9 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P53708 adhesion adhesion ITGA8 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE MCAM;Adhesome;OmniPath generic functional resource_specific ITGA8 protein 3 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P53708 matrix_adhesion matrix_adhesion ITGA8 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA8 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P53708 receptor receptor ITGA8 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA8 protein 10 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P56199 adhesion adhesion ITGA1 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGA1 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P56199 matrix_adhesion matrix_adhesion ITGA1 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA1 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 P56199 receptor receptor ITGA1 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;ICELLNET;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA1 protein 10 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q13683 adhesion adhesion ITGA7 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Adhesome;OmniPath generic functional resource_specific ITGA7 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q13683 matrix_adhesion matrix_adhesion ITGA7 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA7 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q13683 receptor receptor ITGA7 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA7 protein 9 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q13797 adhesion adhesion ITGA9 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE MCAM;Adhesome;OmniPath generic functional resource_specific ITGA9 protein 3 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q13797 cell_adhesion cell_adhesion ITGA9 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite ITGA9 protein 0 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q13797 matrix_adhesion matrix_adhesion ITGA9 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA9 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q13797 receptor receptor ITGA9 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;HPMR;ICELLNET;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA9 protein 10 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q14118 receptor receptor DAG1 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE CellCellInteractions;CellPhoneDB;OmniPath generic functional resource_specific DAG1 protein 2 FALSE TRUE TRUE TRUE FALSE
adhesion adhesion A4D0S4 Q496J9 transporter transporter SV2C LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite SV2C protein 0 FALSE TRUE FALSE FALSE FALSE
adhesion adhesion A4D0S4 Q7L0J3 transporter transporter SV2A LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Surfaceome;OmniPath generic functional resource_specific SV2A protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q7L1I2 transporter transporter SV2B LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite SV2B protein 0 FALSE TRUE FALSE FALSE FALSE
adhesion adhesion A4D0S4 Q9UKX5 adhesion adhesion ITGA11 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE MCAM;Adhesome;OmniPath generic functional resource_specific ITGA11 protein 3 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q9UKX5 matrix_adhesion matrix_adhesion ITGA11 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific ITGA11 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion A4D0S4 Q9UKX5 receptor receptor ITGA11 LAMB4 1 1 0 1 1 0 Wang 0 0 1 OmniPath generic functional composite LAMB4 protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;CellCellInteractions;CellPhoneDB;HPMR;Surfaceome;Ramilowski2015;LRdb;OmniPath generic functional resource_specific ITGA11 protein 8 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion COMPLEX:P05106_P06756 P16284 adhesion adhesion PECAM1 ITGAV_ITGB3 1 0 0 0 0 0 Baccin2019 Baccin2019:7542249 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGAV_ITGB3 complex 2 TRUE TRUE FALSE TRUE FALSE HGNC;MCAM;OmniPath generic functional resource_specific PECAM1 protein 4 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion COMPLEX:P05106_P06756 P16284 cell_adhesion cell_adhesion PECAM1 ITGAV_ITGB3 1 0 0 0 0 0 Baccin2019 Baccin2019:7542249 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGAV_ITGB3 complex 2 TRUE TRUE FALSE TRUE FALSE Zhong2015;HGNC;OmniPath generic functional resource_specific PECAM1 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion COMPLEX:P05106_P06756 P16284 receptor receptor PECAM1 ITGAV_ITGB3 1 0 0 0 0 0 Baccin2019 Baccin2019:7542249 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGAV_ITGB3 complex 2 TRUE TRUE FALSE TRUE FALSE iTALK;EMBRACE;CellPhoneDB;GO_Intercell;Ramilowski2015;LRdb;Baccin2019;OmniPath generic functional resource_specific PECAM1 protein 7 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion COMPLEX:P05106_P06756 Q14773 adhesion adhesion ICAM4 ITGAV_ITGB3 1 0 0 0 0 0 Baccin2019 Baccin2019:16988024 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGAV_ITGB3 complex 2 TRUE TRUE FALSE TRUE FALSE HGNC;MCAM;OmniPath generic functional resource_specific ICAM4 protein 4 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion COMPLEX:P05106_P06756 Q14773 cell_adhesion cell_adhesion ICAM4 ITGAV_ITGB3 1 0 0 0 0 0 Baccin2019 Baccin2019:16988024 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGAV_ITGB3 complex 2 TRUE TRUE FALSE TRUE FALSE Zhong2015;HGNC;OmniPath generic functional resource_specific ICAM4 protein 2 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion COMPLEX:P05106_P08514 Q14773 adhesion adhesion ICAM4 ITGA2B_ITGB3 1 0 0 0 0 0 Baccin2019 Baccin2019:16988024 1 1 1 OmniPath generic functional composite COMPLEX:ITGA2B_ITGB3 complex 1 TRUE TRUE FALSE TRUE FALSE HGNC;MCAM;OmniPath generic functional resource_specific ICAM4 protein 4 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion COMPLEX:P05106_P08514 Q14773 cell_adhesion cell_adhesion ICAM4 ITGA2B_ITGB3 1 0 0 0 0 0 Baccin2019 Baccin2019:16988024 1 1 1 OmniPath generic functional composite COMPLEX:ITGA2B_ITGB3 complex 1 TRUE TRUE FALSE TRUE FALSE Zhong2015;HGNC;OmniPath generic functional resource_specific ICAM4 protein 2 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion COMPLEX:P05556_P13612 P08571 receptor receptor CD14 ITGA4_ITGB1 1 0 0 0 0 0 Baccin2019 Baccin2019:17274987 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGA4_ITGB1 complex 2 TRUE TRUE FALSE TRUE FALSE CellCellInteractions;HGNC;GO_Intercell;Baccin2019;OmniPath generic functional resource_specific CD14 protein 4 FALSE TRUE TRUE FALSE TRUE
adhesion adhesion COMPLEX:P05556_P13612 P57087 adhesion adhesion JAM2 ITGA4_ITGB1 1 0 0 0 0 0 Baccin2019;CellPhoneDB 0 0 2 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGA4_ITGB1 complex 2 TRUE TRUE FALSE TRUE FALSE HGNC;OmniPath generic functional resource_specific JAM2 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion COMPLEX:P05556_P13612 P57087 cell_adhesion cell_adhesion JAM2 ITGA4_ITGB1 1 0 0 0 0 0 Baccin2019;CellPhoneDB 0 0 2 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGA4_ITGB1 complex 2 TRUE TRUE FALSE TRUE FALSE HGNC;OmniPath generic functional resource_specific JAM2 protein 1 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion COMPLEX:P05556_P13612 P57087 tight_junction tight_junction JAM2 ITGA4_ITGB1 1 0 0 0 0 0 Baccin2019;CellPhoneDB 0 0 2 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGA4_ITGB1 complex 2 TRUE TRUE FALSE TRUE FALSE GO_Intercell;Zhong2015;OmniPath generic functional resource_specific JAM2 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion COMPLEX:P05556_P13612 Q14773 adhesion adhesion ICAM4 ITGA4_ITGB1 1 0 0 0 0 0 Baccin2019 Baccin2019:16988024 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGA4_ITGB1 complex 2 TRUE TRUE FALSE TRUE FALSE HGNC;MCAM;OmniPath generic functional resource_specific ICAM4 protein 4 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion COMPLEX:P05556_P13612 Q14773 cell_adhesion cell_adhesion ICAM4 ITGA4_ITGB1 1 0 0 0 0 0 Baccin2019 Baccin2019:16988024 1 1 1 Adhesome;OmniPath generic functional resource_specific COMPLEX:ITGA4_ITGB1 complex 2 TRUE TRUE FALSE TRUE FALSE Zhong2015;HGNC;OmniPath generic functional resource_specific ICAM4 protein 2 TRUE TRUE TRUE TRUE FALSE
adhesion adhesion O00548 P46531 adhesion adhesion NOTCH1 DLL1 1 1 0 1 1 0 Baccin2019;CellPhoneDB;EMBRACE;Fantom5_LRdb;HPMR_LRdb;HPRD;HPRD_LRdb;KEGG-MEDICUS;Kirouac2010;LRdb;NetPath;Ramilowski2015;Ramilowski2015_Baccin2019;SIGNOR;SPIKE;UniProt_LRdb;Wang;iTALK Baccin2019:1006133;Baccin2019:98194281;CellPhoneDB:22353464;HPRD:11006133;LRdb:11;LRdb:9819428;NetPath:11006133;SIGNOR:16140393;SPIKE:11006133;SPIKE:17537801 10 8 13 MCAM;OmniPath generic functional resource_specific DLL1 protein 1 TRUE TRUE FALSE TRUE FALSE OmniPath generic functional composite NOTCH1 protein 1 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O00548 P46531 cell_adhesion cell_adhesion NOTCH1 DLL1 1 1 0 1 1 0 Baccin2019;CellPhoneDB;EMBRACE;Fantom5_LRdb;HPMR_LRdb;HPRD;HPRD_LRdb;KEGG-MEDICUS;Kirouac2010;LRdb;NetPath;Ramilowski2015;Ramilowski2015_Baccin2019;SIGNOR;SPIKE;UniProt_LRdb;Wang;iTALK Baccin2019:1006133;Baccin2019:98194281;CellPhoneDB:22353464;HPRD:11006133;LRdb:11;LRdb:9819428;NetPath:11006133;SIGNOR:16140393;SPIKE:11006133;SPIKE:17537801 10 8 13 MCAM;OmniPath generic functional resource_specific DLL1 protein 1 TRUE TRUE FALSE TRUE FALSE Zhong2015;OmniPath generic functional resource_specific NOTCH1 protein 1 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O00548 P46531 receptor receptor NOTCH1 DLL1 1 1 0 1 1 0 Baccin2019;CellPhoneDB;EMBRACE;Fantom5_LRdb;HPMR_LRdb;HPRD;HPRD_LRdb;KEGG-MEDICUS;Kirouac2010;LRdb;NetPath;Ramilowski2015;Ramilowski2015_Baccin2019;SIGNOR;SPIKE;UniProt_LRdb;Wang;iTALK Baccin2019:1006133;Baccin2019:98194281;CellPhoneDB:22353464;HPRD:11006133;LRdb:11;LRdb:9819428;NetPath:11006133;SIGNOR:16140393;SPIKE:11006133;SPIKE:17537801 10 8 13 MCAM;OmniPath generic functional resource_specific DLL1 protein 1 TRUE TRUE FALSE TRUE FALSE iTALK;CellCellInteractions;EMBRACE;HGNC;CellPhoneDB;HPMR;ICELLNET;Surfaceome;Ramilowski2015;Kirouac2010;LRdb;Baccin2019;SignaLink_function;OmniPath generic functional resource_specific NOTCH1 protein 13 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O00548 Q04721 receptor receptor NOTCH2 DLL1 1 1 0 1 1 0 Baccin2019;BioGRID;CellPhoneDB;Fantom5_LRdb;HPRD;HPRD_LRdb;KEGG-MEDICUS;LRdb;NetPath;Ramilowski2015;Ramilowski2015_Baccin2019;SIGNOR;UniProt_LRdb;Wang;iTALK Baccin2019:10958687;BioGRID:9244302;CellPhoneDB:22353464;HPRD:10958687;LRdb:10958687;NetPath:10958687;SIGNOR:16140393;SIGNOR:23111325 8 5 11 MCAM;OmniPath generic functional resource_specific DLL1 protein 1 TRUE TRUE FALSE TRUE FALSE iTALK;Almen2009;CellCellInteractions;HGNC;CellPhoneDB;GO_Intercell;HPMR;ICELLNET;Surfaceome;Ramilowski2015;LRdb;Baccin2019;SignaLink_function;OmniPath generic functional resource_specific NOTCH2 protein 13 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O00548 Q99466 receptor receptor NOTCH4 DLL1 1 1 0 1 1 0 CellPhoneDB;EMBRACE;KEGG-MEDICUS;LRdb;SIGNOR;UniProt_LRdb;Wang;iTALK CellPhoneDB:22353464;SIGNOR:16140393 2 2 7 MCAM;OmniPath generic functional resource_specific DLL1 protein 1 TRUE TRUE FALSE TRUE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;HGNC;CellPhoneDB;GO_Intercell;HPMR;ICELLNET;Surfaceome;Ramilowski2015;LRdb;Baccin2019;SignaLink_function;OmniPath generic functional resource_specific NOTCH4 protein 14 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O00548 Q9UM47 receptor receptor NOTCH3 DLL1 1 1 0 1 1 0 Baccin2019;CancerCellMap;CellPhoneDB;EMBRACE;Fantom5_LRdb;HPRD;HPRD_LRdb;KEGG-MEDICUS;LRdb;NetPath;Ramilowski2015;Ramilowski2015_Baccin2019;SIGNOR;UniProt_LRdb;Wang;iTALK Baccin2019:11006133;Baccin2019:12482954;CancerCellMap:11006133;CellPhoneDB:22353464;HPRD:11006133;HPRD:12482954;LRdb:11;LRdb:12482954;NetPath:11006133;SIGNOR:11006133;SIGNOR:16140393 11 5 12 MCAM;OmniPath generic functional resource_specific DLL1 protein 1 TRUE TRUE FALSE TRUE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;HGNC;CellPhoneDB;HPMR;ICELLNET;Surfaceome;Ramilowski2015;LRdb;Baccin2019;SignaLink_function;OmniPath generic functional resource_specific NOTCH3 protein 13 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O14522 O60716 adhesion adhesion CTNND1 PTPRT 1 0 0 0 0 0 DEPOD DEPOD:16973135 1 1 1 OmniPath generic functional composite PTPRT protein 1 TRUE TRUE FALSE TRUE FALSE OmniPath generic functional composite CTNND1 protein 1 TRUE TRUE FALSE FALSE FALSE
adhesion adhesion O14522 O60716 cell_adhesion cell_adhesion CTNND1 PTPRT 1 0 0 0 0 0 DEPOD DEPOD:16973135 1 1 1 OmniPath generic functional composite PTPRT protein 1 TRUE TRUE FALSE TRUE FALSE Zhong2015;OmniPath generic functional resource_specific CTNND1 protein 1 TRUE TRUE FALSE FALSE FALSE
adhesion adhesion O14522 P12830 adhesion adhesion CDH1 PTPRT 1 0 0 0 0 0 DEPOD DEPOD:16973135 1 1 1 OmniPath generic functional composite PTPRT protein 1 TRUE TRUE FALSE TRUE FALSE HGNC;OmniPath generic functional resource_specific CDH1 protein 3 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14522 P12830 cell_adhesion cell_adhesion CDH1 PTPRT 1 0 0 0 0 0 DEPOD DEPOD:16973135 1 1 1 OmniPath generic functional composite PTPRT protein 1 TRUE TRUE FALSE TRUE FALSE Zhong2015;HGNC;OmniPath generic functional resource_specific CDH1 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14594 O75056 adhesion adhesion SDC3 NCAN 1 0 0 0 0 0 EMBRACE;Fantom5_LRdb;LRdb;iTALK 0 0 3 OmniPath generic functional composite NCAN protein 1 TRUE TRUE TRUE FALSE FALSE OmniPath generic functional composite SDC3 protein 1 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14594 O75056 cell_adhesion cell_adhesion SDC3 NCAN 1 0 0 0 0 0 EMBRACE;Fantom5_LRdb;LRdb;iTALK 0 0 3 OmniPath generic functional composite NCAN protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;OmniPath generic functional resource_specific SDC3 protein 1 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14594 O75056 receptor receptor SDC3 NCAN 1 0 0 0 0 0 EMBRACE;Fantom5_LRdb;LRdb;iTALK 0 0 3 OmniPath generic functional composite NCAN protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;Almen2009;EMBRACE;HPMR;Ramilowski2015;LRdb;Baccin2019;OmniPath generic functional resource_specific SDC3 protein 7 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O14594 P19022 adhesion adhesion CDH2 NCAN 1 0 0 0 0 0 EMBRACE;Fantom5_LRdb;LRdb;iTALK 0 0 3 OmniPath generic functional composite NCAN protein 1 TRUE TRUE TRUE FALSE FALSE HGNC;OmniPath generic functional resource_specific CDH2 protein 4 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14594 P19022 cell_adhesion cell_adhesion CDH2 NCAN 1 0 0 0 0 0 EMBRACE;Fantom5_LRdb;LRdb;iTALK 0 0 3 OmniPath generic functional composite NCAN protein 1 TRUE TRUE TRUE FALSE FALSE Zhong2015;Almen2009;HGNC;OmniPath generic functional resource_specific CDH2 protein 3 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14594 P19022 receptor receptor CDH2 NCAN 1 0 0 0 0 0 EMBRACE;Fantom5_LRdb;LRdb;iTALK 0 0 3 OmniPath generic functional composite NCAN protein 1 TRUE TRUE TRUE FALSE FALSE iTALK;CellCellInteractions;EMBRACE;GO_Intercell;Baccin2019;OmniPath generic functional resource_specific CDH2 protein 5 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O14713 P05106 adhesion adhesion ITGB3 ITGB1BP1 1 0 1 1 0 1 SIGNOR SIGNOR:19118207 1 1 1 OmniPath generic functional composite ITGB1BP1 protein 1 TRUE TRUE FALSE TRUE FALSE Adhesome;OmniPath generic functional resource_specific ITGB3 protein 2 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14713 P05106 matrix_adhesion matrix_adhesion ITGB3 ITGB1BP1 1 0 1 1 0 1 SIGNOR SIGNOR:19118207 1 1 1 OmniPath generic functional composite ITGB1BP1 protein 1 TRUE TRUE FALSE TRUE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB3 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O14713 P05106 receptor receptor ITGB3 ITGB1BP1 1 0 1 1 0 1 SIGNOR SIGNOR:19118207 1 1 1 OmniPath generic functional composite ITGB1BP1 protein 1 TRUE TRUE FALSE TRUE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;Baccin2019;OmniPath generic functional resource_specific ITGB3 protein 11 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O14713 P05107 adhesion adhesion ITGB2 ITGB1BP1 1 0 1 1 0 1 SIGNOR SIGNOR:19118207 1 1 1 OmniPath generic functional composite ITGB1BP1 protein 1 TRUE TRUE FALSE TRUE FALSE MCAM;Adhesome;OmniPath generic functional resource_specific ITGB2 protein 3 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14713 P05107 cell_adhesion cell_adhesion ITGB2 ITGB1BP1 1 0 1 1 0 1 SIGNOR SIGNOR:19118207 1 1 1 OmniPath generic functional composite ITGB1BP1 protein 1 TRUE TRUE FALSE TRUE FALSE OmniPath generic functional composite ITGB2 protein 0 TRUE TRUE FALSE TRUE FALSE
adhesion adhesion O14713 P05107 matrix_adhesion matrix_adhesion ITGB2 ITGB1BP1 1 0 1 1 0 1 SIGNOR SIGNOR:19118207 1 1 1 OmniPath generic functional composite ITGB1BP1 protein 1 TRUE TRUE FALSE TRUE FALSE Zhong2015;OmniPath generic functional resource_specific ITGB2 protein 1 FALSE TRUE FALSE TRUE FALSE
adhesion adhesion O14713 P05107 receptor receptor ITGB2 ITGB1BP1 1 0 1 1 0 1 SIGNOR SIGNOR:19118207 1 1 1 OmniPath generic functional composite ITGB1BP1 protein 1 TRUE TRUE FALSE TRUE FALSE iTALK;Almen2009;CellCellInteractions;EMBRACE;CellPhoneDB;GO_Intercell;HPMR;Surfaceome;Ramilowski2015;LRdb;Baccin2019;OmniPath generic functional resource_specific ITGB2 protein 11 FALSE TRUE FALSE TRUE FALSE

There are 44 columns to explore:

sort(colnames(icn))
##  [1] "aspect_intercell_source"                       
##  [2] "aspect_intercell_target"                       
##  [3] "category_intercell_source"                     
##  [4] "category_intercell_target"                     
##  [5] "category_source_intercell_source"              
##  [6] "category_source_intercell_target"              
##  [7] "consensus_direction"                           
##  [8] "consensus_inhibition"                          
##  [9] "consensus_score_intercell_source"              
## [10] "consensus_score_intercell_target"              
## [11] "consensus_stimulation"                         
## [12] "curation_effort"                               
## [13] "database_intercell_source"                     
## [14] "database_intercell_target"                     
## [15] "dip_url"                                       
## [16] "entity_type_intercell_source"                  
## [17] "entity_type_intercell_target"                  
## [18] "genesymbol_intercell_source"                   
## [19] "genesymbol_intercell_target"                   
## [20] "is_directed"                                   
## [21] "is_inhibition"                                 
## [22] "is_stimulation"                                
## [23] "n_references"                                  
## [24] "n_resources"                                   
## [25] "parent_intercell_source"                       
## [26] "parent_intercell_target"                       
## [27] "plasma_membrane_peripheral_intercell_source"   
## [28] "plasma_membrane_peripheral_intercell_target"   
## [29] "plasma_membrane_transmembrane_intercell_source"
## [30] "plasma_membrane_transmembrane_intercell_target"
## [31] "receiver_intercell_source"                     
## [32] "receiver_intercell_target"                     
## [33] "references"                                    
## [34] "scope_intercell_source"                        
## [35] "scope_intercell_target"                        
## [36] "secreted_intercell_source"                     
## [37] "secreted_intercell_target"                     
## [38] "source"                                        
## [39] "source_genesymbol"                             
## [40] "sources"                                       
## [41] "target"                                        
## [42] "target_genesymbol"                             
## [43] "transmitter_intercell_source"                  
## [44] "transmitter_intercell_target"

Show how many references support each record#

There are 13,126 records with 0 references, and 17,139 records with at least 1 reference.

This histogram summarizes the number of records (y-axis) with each number of supporting references (x-axis).

library(ggplot2)

ggplot(icn) +
  geom_histogram(aes(n_references)) +
  scale_y_continuous(trans = "log10")

plot of chunk unnamed-chunk-9

I'm not sure what the ID numbers mean, but it looks like there are some references and databases listed here:

icn$references[which(icn$n_references > 2)[1:5]]
## [1] "Baccin2019:1006133;Baccin2019:98194281;CellPhoneDB:22353464;HPRD:11006133;LRdb:11;LRdb:9819428;NetPath:11006133;SIGNOR:16140393;SPIKE:11006133;SPIKE:17537801"                         
## [2] "Baccin2019:1006133;Baccin2019:98194281;CellPhoneDB:22353464;HPRD:11006133;LRdb:11;LRdb:9819428;NetPath:11006133;SIGNOR:16140393;SPIKE:11006133;SPIKE:17537801"                         
## [3] "Baccin2019:1006133;Baccin2019:98194281;CellPhoneDB:22353464;HPRD:11006133;LRdb:11;LRdb:9819428;NetPath:11006133;SIGNOR:16140393;SPIKE:11006133;SPIKE:17537801"                         
## [4] "Baccin2019:10958687;BioGRID:9244302;CellPhoneDB:22353464;HPRD:10958687;LRdb:10958687;NetPath:10958687;SIGNOR:16140393;SIGNOR:23111325"                                                 
## [5] "Baccin2019:11006133;Baccin2019:12482954;CancerCellMap:11006133;CellPhoneDB:22353464;HPRD:11006133;HPRD:12482954;LRdb:11;LRdb:12482954;NetPath:11006133;SIGNOR:11006133;SIGNOR:16140393"

Filter the table#

Let's filter the table to source-target pairs where the consensus score for the source is greater than 4. Then we can take a subset of the columns, to simplify the table.

omni <- icn %>%
  dplyr::filter(consensus_score_intercell_source > 4) %>%
  dplyr::select(
    target_genesymbol,
    source_genesymbol,
    is_stimulation,
    consensus_score_intercell_source
  ) %>%
  unique
head(omni)
## # A tibble: 6 x 4
##   target_genesymbol source_genesymbol is_stimulation consensus_score_intercell_…
##   <chr>             <chr>                      <int>                       <int>
## 1 NRXN1             NLGN3                          0                           5
## 2 NRXN2             NLGN3                          1                           5
## 3 NRXN3             NLGN3                          1                           5
## 4 NRXN1             NLGN3                          1                           5
## 5 MUSK              AGRN                           1                           5
## 6 LRP4              AGRN                           0                           5

Suppose we have a few genes of interest:

my_genes <- c(
  "CD274", "CXCL1", "CXCL13", "CXCR3", "CXCR5"
)

Are the genes in this table?

Yes, and it looks like CXCR3 and CXCR5 are labeled as “target” genes:

my_genes[my_genes %in% omni$target_genesymbol]
## [1] "CXCR3" "CXCR5"

While CD274, CXCL1, CXCL13 are labeld as “source” genes:

my_genes[my_genes %in% omni$source_genesymbol]
## [1] "CD274"  "CXCL1"  "CXCL13"

Learn more#

Please see the OmniPath website for more details: https://omnipathdb.org/

There is a lot to explore: