Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.11.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02486	0.932
27DAP/17DAP	0.96191	0.964
39DAP/27DAP	0.95882	0.682
41DAP/39DAP	1.13655	0.56
42DAP/41DAP	0.95055	1
43DAP/42DAP	0.99527	0.937
47DAP/43DAP	1.12574	0.889
52DAP/47DAP	0.96304	0.865
57DAP/52DAP	1.00559	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.58523	0.092
17DAP/reference	N/A	N/A
27DAP/reference	0.78996
39DAP/reference	0.91837	0.587
41DAP/reference	1.63592	0.012
42DAP/reference	1.05904	0.449
43DAP/reference	0.37112
47DAP/reference	0.83241	0.021
52DAP/reference	0.41008	0.03
57DAP/reference	0.78078

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97849
27DAP/17DAP	1.05921	0.867
39DAP/27DAP	1.0523	0.672
41DAP/39DAP	1.05074	0.773
42DAP/41DAP	1.04096	0.795
43DAP/42DAP	1.01708	0.746
47DAP/43DAP	0.96291	0.823
52DAP/47DAP	0.96445	0.837
57DAP/52DAP	0.95149	0.359
57DAP/7DAP	0.87153

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92965	0.183
17DAP/reference	0.98415	0.518
27DAP/reference	0.99625	0.656
39DAP/reference	1.01335	0.705
41DAP/reference	0.95336	0.223
42DAP/reference	0.93565	0.026
43DAP/reference	0.96156	0.334
47DAP/reference	0.98197	0.222
52DAP/reference	0.92839	0.213
57DAP/reference	0.98869	0.629

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99918	0.93
17DAP/reference	0.95706	0.474
27DAP/reference	0.98709	0.686
39DAP/reference	1.04672	0.725
41DAP/reference	0.98812	0.519
42DAP/reference	1.17909	1
43DAP/reference	1.10364	0.192
47DAP/reference	1.10734	0.282
52DAP/reference	1.09583	0.471
57DAP/reference	1.39834	0.538

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94221	0.112
17DAP/reference	0.94331	0.214
27DAP/reference	0.97505	0.337
39DAP/reference	1.03767	0.218
41DAP/reference	0.95492	0.027
42DAP/reference	1.47894	0.51
43DAP/reference	0.96843	0.416
47DAP/reference	0.99215	0.626
52DAP/reference	0.94722	0.31
57DAP/reference	0.86612	0.288

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9937	1
26DAP/20DAP	1.00915	1
34DAP/26DAP	1.11268	0.819
51DAP/34DAP	0.98496	0.893
52DAP/51DAP	0.99319	1
53DAP/52DAP	0.93732
55DAP/53DAP	0.97473	0.775
57DAP/55DAP	0.98143	0.902
62DAP/57DAP	0.87554	0.28
68DAP/62DAP	1.00921	0.914
68DAP/14DAP	0.91397	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92146	0.198

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.82617	0.41
Mature Green Tomato/Ripe Tomato	0.72577	0.2
Immature Eggplant/Mature Eggplant	0.78142	0.067
Ripe Pepper/Ripe Tomato	3.22629	0.256
Mature Eggplant/Ripe Tomato	1.9727	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.98379	0.961
1-1-2/M82	0.87385	0.958
12-2/M82	0.90173	0.955
12-4/M82	0.89163	1
1-3/M82	1.02236	1
2-1-1/M82	0.94301	0.683
2-1/M82	0.92137
2-6/M82	0.96496	1
3-2/M82	0.93453	1
4-1-1/M82	0.95411	1
4-1/M82	0.84545	0.737
4-3-2/M82	1.00421	1
4-3/M82	0.93405	1
5-3/M82	1.04819	1
6-2/M82	1.00121	1
6-3/M82	1.01591	1
7-1/M82	0.97073	0.452
7-2/M82	1.08797	1
9-3-2/M82	0.92306	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.93079	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.87697	0.294
IL12-4/WTpooled	1.30574	0.785
IL1-4/WTpooled	0.84979	0.444
WT/WTpooled	0.99622	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.0729	1

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	N/A	N/A
DC3000/delta hrp 6h	1.07622	1
DC3000/delta hrp 12h	0.98013	1
DC3000/delta hrp 24h	1.09111	0.453

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.00929	0.648
DC3000 delta B/DC3000 delta AB	1.09197	0.349

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.20866	0.254
Exp 36h	0.63738	0.426
Exp 60h	1.1011	1

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.99916	1
Var 0h	0.96468	1
Var 12h I row2-row1	1.1106	0.22
Var 12h NI row2-row1	0.97885	0.906
Var 36h I row2-row1	0.91854	1
Var 36h NI row2-row1	1.0186	1
Var 60h I row2-row1	1.25756	1
Var 60h NI row2-row1	1.10022	0.904
Time course 0hI-0hNI	1.04024	0.867
Time course 12hI-12hNI	0.99041	0.978
Time course 36hI-36hNI	0.98338	0.559
Time course 60hI-60hNI	1.02072	0.495

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.88401	0.26
transgenic ySAMdc/azygous control (breaker)	1.12081	1
transgenic ySAMdc/azygous control (red)	1.16075	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.95301	1
Manapal/WT (red)	1.00849	1