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BlishLab / scriabin

Analysis of cell-cell communication at single-cell resolution
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Bizarre Results for Cell Co-culture Data Set #22

Open DarioS opened 7 months ago

DarioS commented 7 months ago

I have a data set which is cancer-fibroblast co-culture of patient derived cells. Many interactions have p-value of 0 in many samples.

> significance[1:20, c(1:7)]

         lr_pair  name OSCC_16-P_pval OSCC_16-M_pval OSCC_20-P_pval OSCC_24-P_pval OSCC_24-M_pval
1  ADAM17=NOTCH1  IP-1              0              0              0              0              0
2     ANXA1=EGFR  IP-1              0              0              0              0              0
3    DLL1=NOTCH1  IP-1              0              0              0              0              0
4    EFNA4=EPHA2  IP-1              0              0              0              0              0
5     EGFR=ERBB3  IP-1              0              0              0              0              0
6      EGFR=TGFA  IP-1              0              0              0              0              0
7    EPHA2=EFNA1  IP-1              0              0              0              0              0
8    ERBB2=ERBB3  IP-1              0              0              0              0              0
9     MDK=PTPRZ1  IP-1              0              0              0              0              0
10   NOTCH1=DLL1  IP-1              0              0              0              0              0
11    WNT3A=FZD5  IP-1              0              0              0              0              0
12  APP=TNFRSF21 IP-10              0              0              0              0              0
13     AREG=EGFR IP-10              0              0              0              0              0
14     BACE2=APP IP-10              0              0              0              0              0
15   BMP7=BMPR1B IP-10              0              0              0              0              0
16     CDH1=EGFR IP-10              0              0              0              0              0
17   DLL1=NOTCH1 IP-10              0              0              0              0              0
18   EFNA1=EPHA1 IP-10              0              0              0              0              0
19   IL20=IL20RB IP-10              0              0              0              0              0
20  IL20=IL22RA1 IP-10              0              0              0              0              0

Why is it so? Also, ERBB2 and ERBB3 are both receptors. Why are receptor-receptor pairs being analysed?