Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.6.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97177	0.779
27DAP/17DAP	1.06001	0.922
39DAP/27DAP	0.94189	0.663
41DAP/39DAP	1.26298	0.612
42DAP/41DAP	0.97555	1
43DAP/42DAP	0.94539	0.801
47DAP/43DAP	1.04941	0.727
52DAP/47DAP	0.80149	0.43
57DAP/52DAP	1.09904	0.748

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96452	0.455
17DAP/reference	0.90847	0.024
27DAP/reference	0.94518	0.147
39DAP/reference	0.90644	0.132
41DAP/reference	0.96487	0.341
42DAP/reference	1.00732	1
43DAP/reference	1.01534	0.866
47DAP/reference	0.98131	0.392
52DAP/reference	1.09833	0.476
57DAP/reference	1.03571	0.31

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28414	0.036
27DAP/17DAP	0.91336	0.475
39DAP/27DAP	0.94467	0.673
41DAP/39DAP	1.04304	0.853
42DAP/41DAP	1.04253	0.763
43DAP/42DAP	0.97517	0.801
47DAP/43DAP	0.96926	0.857
52DAP/47DAP	0.92455	0.603
57DAP/52DAP	0.73194	0.294
57DAP/7DAP	1.25362

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87647	0.224
17DAP/reference	1.13795	0.477
27DAP/reference	0.99506	0.698
39DAP/reference	1.00582	0.745
41DAP/reference	1.03663	1
42DAP/reference	0.84984	0.136
43DAP/reference	0.88597	0.145
47DAP/reference	1.05127	0.791
52DAP/reference	0.99531	0.74
57DAP/reference	0.90333	0.26

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04852	0.642
17DAP/reference	1.09678	0.098
27DAP/reference	1.13746	0.133
39DAP/reference	1.06235	0.463
41DAP/reference	1.01966	0.925
42DAP/reference	1.03442	0.777
43DAP/reference	1.08158	0.59
47DAP/reference	0.99687	0.714
52DAP/reference	1.03387	0.596
57DAP/reference	1.009	0.874

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01557	1
17DAP/reference	1.02758	0.689
27DAP/reference	0.97678
39DAP/reference	1.10352	0.275
41DAP/reference	1.54421	0.065
42DAP/reference	1.23369	0.184
43DAP/reference	1.42227	0.016
47DAP/reference	1.0652	0.171
52DAP/reference	1.05769	0.705
57DAP/reference	1.06608	0.581

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97929	1
26DAP/20DAP	1.06282	0.806
34DAP/26DAP	1.08275	1
51DAP/34DAP	0.9372	0.649
52DAP/51DAP	0.94222	1
53DAP/52DAP	0.96614	0.824
55DAP/53DAP	0.91311	0.263
57DAP/55DAP	1.07838	0.195
62DAP/57DAP	1.02304	1
68DAP/62DAP	0.84745	0.464
68DAP/14DAP	1.20934	0.131

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.56533	0.03

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.79944	0.272
Mature Green Tomato/Ripe Tomato	0.96857	0.487
Immature Eggplant/Mature Eggplant	1.18943	0.248
Ripe Pepper/Ripe Tomato	0.62863	1
Mature Eggplant/Ripe Tomato	0.88463	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05882	0.877
1-1-2/M82	0.89913	1
12-2/M82	0.98402	1
12-4/M82	0.93385	1
1-3/M82	0.92523	0.501
2-1-1/M82	N/A	N/A
2-1/M82	1.02941
2-6/M82	1.19179	0.405
3-2/M82	0.9762	1
4-1-1/M82	1.00089	1
4-1/M82	1.04255	0.512
4-3-2/M82	0.92107	1
4-3/M82	0.95995	1
5-3/M82	1.02823	1
6-2/M82	1.25701
6-3/M82	0.90574
7-1/M82	1.0373	1
7-2/M82	0.97397	1
9-3-2/M82	0.95854	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99646	1
IL2-6/WTpooled	1.04607	0.788
IL7-5/WTpooled	0.92577	1
IL7-3/WTpooled	0.91912	0.31
IL12-4/WTpooled	0.78997	0.566
IL1-4/WTpooled	1.27176	0.426
WT/WTpooled	0.87783	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	0.74682	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94494	1
DC3000/delta hrp 6h	1.13541	1
DC3000/delta hrp 12h	0.91041	1
DC3000/delta hrp 24h	1.02407	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.82342
DC3000 delta B/DC3000 delta AB	0.87833	0.543

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99828	1
Exp 36h	1.4402	1
Exp 60h	1.11867	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98513	1
Var 0h	1.1235	0.223
Var 12h I row2-row1	0.94722	0.77
Var 12h NI row2-row1	0.85882	0.546
Var 36h I row2-row1	1.20543	1
Var 36h NI row2-row1	1.06948	0.482
Var 60h I row2-row1	1.08733	0.543
Var 60h NI row2-row1	0.88259	0.818
Time course 0hI-0hNI	1.00636	0.867
Time course 12hI-12hNI	0.93591	0.454
Time course 36hI-36hNI	0.92408	0.236
Time course 60hI-60hNI	0.90231	0.081

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)	0.93816	0.567
transgenic ySAMdc/azygous control (breaker)	0.94765	0.173
transgenic ySAMdc/azygous control (red)	1.05234	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03837	0.077

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)	0.90672	0.172
Manapal/WT (break)	0.88713	1
Manapal/WT (red)	1.16386	0.164