Differentiation Landscape


All inferred binary fate choices were integrated with normal fate progression to generate a landscape of lineage differentiation with 56 trajectories and 32 types of regulated fate choices. This directed graph summarizes all possible trajectories a cell can take to differentiate into a specific fate and the corresponding regulatory switch genes that determine the differentiation path along the trajectories.

Nodes represent cell fates and arrows represent trajectories of differentiation. Black arrows represent trajectories observed during normal development; green arrows represent alternative trajectories observed due to gene perturbation. All detected alternative trajectories are labeled by number. Each open circle represents a decision point of cell fate choice. Regulators of the fate choice between default and alternative trajectories are shown below.

Trajectory Alternative Path Normal Path Genes
1 P0-to-ABp P0-to-AB cdc-25.1,cls-2,div-1,puf-3,rfc-3,zyg-11
2 P0-to-C P0-to-AB mex-3
3 P0-to-EMS P0-to-AB mbk-2, mex-5, par-3, zyg-11
4 P0-to-P2 P0-to-P1 cdc-25.1, div-1
5 AB-to-ABa AB-to-ABp apx-1,atx-2,glp-1,lag-1,par-2,par-6,pie-1,pkc-3,pos-1,rga-3,sel-8
6 AB-to-ABp AB-to-ABa F23F1.5,ceh-24,csn-4,cul-2,npp-4,ran-4,wwp-1
7 P1-to-C P1-to-EMS F44B9.8,Y53F4B.22,atx-2,cdc-37,mbk-2,oma-1/2,skn-1,tsr-1
8 P1-to-EMS P1-to-P2 arp-11,par-2,par-6,pie-1,pkc-3
9 ABa-to-ABal ABa-to-ABar atx-2,camt-1,ceh-24,cpl-1,cul-1,cul-3,gld-2,gsk-3,hmp-2,let-502,lin-23,mei-1,mom-2,mom-5,oma-1/2,par-2,par-3,pos-1,ppfr-4,puf-3,rga-3,skr-1/2,tag-256,tat-5,uba-1
10 ABal-to-ABarp ABal-to-ABala cul-3
11 ABal-to-ABarp ABal-to-ABalp cdc-37,glp-1,lag-1,oma-1/2,par-6,pkc-3,ran-4,sel-8,skn-1
12 ABal-to-ABara ABal-to-ABalp T11G6.8, rad-51
13 ABal-to-ABalp ABal-to-ABala par-3
14 ABar-to-ABala ABar-to-ABara glp-1, lag-1, par-6, sel-8, skn-1
15 ABal-to-ABara ABal-to-ABala arp-11,atx-2,cdc-37,ceh-24,chaf-2,chk-1,cpl-1,cul-1,dlc-1,dli-1,gld-2,gsk-3,hda-1,let-502,nud-1,par-3,rba-1,rga-3,skr-1/2,tat-5,ubc-12,vps-4
16 ABar-to-ABara ABar-to-ABarp gpb-1
17 ABar-to-ABalp ABar-to-ABarp ceh-24, gpb-1, ubc-12
18 ABpl-to-ABplp ABpl-to-ABpla drh-3
19 ABpl-to-ABpra ABpl-to-ABplp cul-3
20 ABpr-to-ABpla ABpr-to-ABpra camt-1,cul-3,gld-2,let-502,lin-23,mei-1,mom-2,mom-5,oma-1/2,ppfr-4,rab-7,ran-4,rga-3,skn-1,skr-1/2,tag-256,tat-5
21 ABpl-to-ABpra ABpl-to-ABpla F35F11.1,ceh-24,cul-3,glp-1,gsk-3,lag-1,nmy-2,npp-4,pad-1,pop-1,rab-5,rga-3,ruvb-1,suf-1,wwp-1,zyg-12
22 ABpr-to-ABpra ABpr-to-ABprp cul-3
23 EMS-to-EMS EMS-to-MS cul-1, lin-23, skr-1/2, zyg-11
24 P2-to-EMS P2-to-C cul-1, gsk-3, lin-23, skr-1/2
25 P2-to-C P2-to-P3 cdc-37
26 P2-to-MS P2-to-C gei-17
27 EMS-to-E EMS-to-MS pop-1
28 EMS-to-MS EMS-to-E gld-2,gsk-3,mom-2,par-2,par-6,pkc-3
29 C-to-C C-to-Cx cul-1, skr-1/2
30 P3-to-P3 P3-to-P4 cul-1, lin-23, skr-1/2
31 P3-to-P4 P3-to-D mex-3
32 P3-to-D P3-to-P4 gld-2, mex-5, src-1