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Table 6 Expression cluster enrichment analysis

From: Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans

Expression clusters over-represented in "dauer enriched" and "exit enriched genes" in C. elegans and P. pacificus
Expression clusters related to dauer larvae, stress response and starvation / feeding
Sl.No. Expression Cluster cel_dauer cel_exit ppa_dauer ppa_exit
1 Wang_Kim_WBPaper00005859_DauerEnriched 10.45 0 0 0
2 Wang_Kim_WBPaper00005859_EarlyGenes 0 5.99 0 10.67
3 Wang_Kim_WBPaper00005859_ClimbingGenes 0 14.58 0 4.62
4 Wang_Kim_WBPaper00005859_LateGenes 0 63.09 0 0
5 WBPaper00024393:strongly_regulated_dauer_genes_UP 1.39 0 0 0
6 WBPaper00024393:strongly_regulated_dauer_genes_DOWN 0 8.49 0 10.85
7 WBPaper00034757:up_by_oxidative_stress 4.2 0 0 0
8 WBPaper00034757:down_by_oxidative_stress 0 6.47 0 6.82
9 WBPaper00035227:heat_shock_regulated 9.74 0 0 0
10 WBPaper00035873:dpy-10_regulated 0 25.06 0 3.89
11 WBPaper00035873:dpy-9_regulated 0 2.02 0 1.57
12 WBPaper00035873:osm-11_regulated 0 2.02 0 1.57
13 WBPaper00035873:osm-7_regulated 0 2.4 0 2.07
14 WBPaper00035873:osm-8_regulated 0 42.83 0 4.45
15 WBPaper00035873:osmotically_regulated 0 0 0 4.65
16 WBPaper00032948:StarveUp2 6.17 0 2.5 0
17 WBPaper00032948:StarveUp3 7.15 0 0 0
18 WBPaper00032948:StarveUp4 10.45 0 0 0
19 WBPaper00032948:FedUp 0 78.95 0 5.12
20 WBPaper00032948:MoltOssilate 0 74.78 0 0
21 WBPaper00032062:age_regulated_genes 0 5.37 0 4.75
Expression clusters related to to pathogen response, RNAi machinery etc.
Sl.No. Expression Cluster cel_dauer cel_exit ppa_dauer ppa_exit
22 WBPaper00028482:PA14_upregulate 0 0 0 2.03
23 WBPaper00028789:PA14_vs_gacA_downregulated_4hr 0 5.9 0 0
24 WBPaper00028789:PA14_vs_gacA_downregulated_8hr 0 6.7 0 0
25 WBPaper00028789:PA14_vs_OP50_downregulated_8hr 0 6.85 0 1.81
26 WBPaper00028789:PA14_vs_OP50_upregulated_4hr 0 0 0 1.4
27 WBPaper00028789:PA14_vs_OP50_upregulated_8hr 0 0 0 2.02
28 WBPaper00030985:Enterococcus_faecalis_upregulated 0 0 0 1.6
29 WBPaper00028789:pmk-1_downregulated 0 0 0 1.46
30 WBPaper00029437:dcr-1_upregulated 3.13 0 0 0
31 WBPaper00029437:rde-4_upregulated 0 0 0 1.69
32 WBPaper00027111:eri-1(mg366)_downregulated 0 2.23 0 0
33 WBPaper00027111:rde-3(r459)_upregulated 0 0 0 1.52
34 WBPaper00035892:KIM5_regulated 0 0 0 4.79
35 WBPaper00035892:KIM5_vs_OP50_Up 0 0 0 2.36
Tissue specific, and other expression clusters
Sl.No. Expression Cluster cel_dauer cel_exit ppa_dauer ppa_exit
36 WBPaper00030839:Embryo_Pan_Neuronal 0 0 6.67 0
37 WBPaper00030839:Larval_Pan_Neuronal 4.75 0 2.71 0
38 WBPaper00031003:0hr_muscle_depleted 0 2.99 0 0
39 WBPaper00031003:24hr_muscle_depleted 0 2.11 0 2.73
40 WBPaper00031003:total_muscle_depleted 0 2.29 0 0
41 WBPaper00031003:total_muscle_enriched 0 0 2.42 0
42 WBPaper00031532:Larva_Pan_Neuronal_Depleted 0 28.03 0 11.41
43 WBPaper00031532:Larva_Pan_Neuronal_Enriched 2.48 0 4.69 0
44 WBPaper00026980:intestine_enriched 0 0 3.46 1.5
45 WBPaper00024671:AFD_AWB_vs_unsorted_downregulated 0 3.02 0 3.59
46 WBPaper00031832:slr-2_regulated 0 0 0 2.75
47 WBPaper00033101:spr-5_regulated 0 6.44 0 0
48 WBPaper00034739:N2lessDR1350 0 39.13 0 0
49 WBPaper00034739:RIL17lessRIL14 0 18.11 0 0
50 WBPaper00035905:FBF-1_Associated 0 0 5.54 0
51 WBPaper00037611:RNP-8-associated 0 0 4.92 0
52 WBPaper00025032:PAL-1_target_genes 0 2.58 0 0
  1. This table lists - log10 transformed p-values of tests for enrichment of dauer and dauer-exit genes from both species for 52 out of 169 expression clusters. These 52 expression clusters passed the FDR corrected p-value threshold of 0.05 for at least one condition. The overlap between dauer enriched clusters and dauer-exit enriched clusters is statistically significant (Fisher’s exact test p-values = 0.0185 and 6.833E-06 respectively).
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