Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.12.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03358	0.927
27DAP/17DAP	0.93533	0.902
39DAP/27DAP	1.04496	0.965
41DAP/39DAP	0.9228	0.743
42DAP/41DAP	1.20202	0.941
43DAP/42DAP	0.78598	0.705
47DAP/43DAP	1.09507	0.979
52DAP/47DAP	0.72291	0.357
57DAP/52DAP	1.00602	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92195	0.205
17DAP/reference	0.85478	0.138
27DAP/reference	0.91981	0.295
39DAP/reference	0.94953	0.412
41DAP/reference	0.95316	0.542
42DAP/reference	0.9144	0.075
43DAP/reference	1.00347	0.904
47DAP/reference	0.92206	0.05
52DAP/reference	1.06453	0.663
57DAP/reference	1.12024	0.355

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23793	0.077
27DAP/17DAP	1.01668	0.943
39DAP/27DAP	1.00596	0.874
41DAP/39DAP	0.95562	0.793
42DAP/41DAP	1.10201	0.508
43DAP/42DAP	0.94897	0.641
47DAP/43DAP	0.93743	0.466
52DAP/47DAP	1.00516	0.982
57DAP/52DAP	1.14011	0.398
57DAP/7DAP	1.14071	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47026	0.036
17DAP/reference	0.93182	0.389
27DAP/reference	1.2304	0.035
39DAP/reference	1.56001	0.042
41DAP/reference	1.24896	0.041
42DAP/reference	1.1267	0.308
43DAP/reference	1.20523	0.034
47DAP/reference	1.34931	0.077
52DAP/reference	1.56361	0.007
57DAP/reference	1.1913	0.288

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07463	0.719
17DAP/reference	0.92671	0.317
27DAP/reference	0.90232	0.119
39DAP/reference	0.85989	0.099
41DAP/reference	0.89762	0.05
42DAP/reference	0.85394	0.055
43DAP/reference	0.82645	0.17
47DAP/reference	0.96203	0.39
52DAP/reference	0.88595	0.259
57DAP/reference	0.86396	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09922	0.244
17DAP/reference	0.9863	0.739
27DAP/reference	1.19463	0.596
39DAP/reference	1.32054	0.012
41DAP/reference	1.13049	0.286
42DAP/reference	1.12094	0.658
43DAP/reference	1.15967	0.555
47DAP/reference	1.11999	0.48
52DAP/reference	1.40873	0.194
57DAP/reference	1.13038	0.771

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.39385	1
26DAP/20DAP	0.79448	0.317
34DAP/26DAP	1.20759	0.819
51DAP/34DAP	0.756	0.061
52DAP/51DAP	0.95594	1
53DAP/52DAP	1.00366	1
55DAP/53DAP	1.01067	0.951
57DAP/55DAP	1.33484	0.854
62DAP/57DAP	0.97072	0.994
68DAP/62DAP	1.40664	0.345
68DAP/14DAP	0.85953	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.75668	0.591

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.97448	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.51919	0.277
IL2-6/WTpooled	0.48153	0.358
IL7-5/WTpooled	0.97253	1
IL7-3/WTpooled	1.70612	1
IL12-4/WTpooled	0.94804	1
IL1-4/WTpooled	0.84951	0.444
WT/WTpooled	0.94121	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	0.89965	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97346	1
DC3000/delta hrp 6h	1.09345	1
DC3000/delta hrp 12h	0.94992	1
DC3000/delta hrp 24h	0.65894	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.95676	0.955
DC3000 delta B/DC3000 delta AB	0.99028	1

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.50521	0.321
Exp 60h	0.83944	0.586

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02322	1
Var 0h	1.20679	0.594
Var 12h I row2-row1	0.80941	0.418
Var 12h NI row2-row1	1.08265	1
Var 36h I row2-row1	1.27832	0.908
Var 36h NI row2-row1	1.37744	0.482
Var 60h I row2-row1	0.98828	1
Var 60h NI row2-row1	1.02744	1
Time course 0hI-0hNI	0.95033	0.659
Time course 12hI-12hNI	0.9496	0.575
Time course 36hI-36hNI	0.78896	0.029
Time course 60hI-60hNI	0.22809	0.005

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)	0.92895	0.348
transgenic ySAMdc/azygous control (breaker)	1.30688	0.161
transgenic ySAMdc/azygous control (red)	1.08253	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95792	0.092

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.35087	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	2.41464	0.096
Manapal/WT (break)	1.99349	0.381
Manapal/WT (red)	2.41412	0.15