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There are 394 CD marker genes. Various resources (BD handbook, Abcam guide) contain information about which cell types express which CD markers. What is the best way to obtain or download this data so that it can be used with programs such as R?

How can we download similar annotation data on expression for any gene or cell type?

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    $\begingroup$ Most of the work of biologist is to characterize the cells and populations, mostly because they reason why they express/use them is mostly unkown. I am not aware of a single database listing markers of a cell line, but it would be quite useful. $\endgroup$
    – llrs
    Oct 17, 2017 at 21:44

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I can offer this as a way to scrape the data from the Abcam resource:

library(rvest)
library(dplyr)

antigens <- read_html("http://www.abcam.com/primary-antibodies/human-cd-antigen-guide") %>% 
  html_node("table") %>% 
  html_table(header = TRUE)

# what targets expressed in "Langerhans" ?
antigens %>% 
  filter(grepl("Langerhans", `Cellular Expression`)) %>% 
  select(`Target Name`)

   Target Name
1         CD1a
2         CD1b
3         CD1c
4         CD1e
5         CD14
6         CD39
7         CD50
8         CD69
9         CD74
10        CD83
11       CD101
12       CD206
13       CD207

The data could be further processed by, for example, splitting the Cellular Expression column on either and or , (comma) to try and make one row per cell type.

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