Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.19.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.06216	0.912
27DAP/17DAP	1.11251	1
39DAP/27DAP	1.12672	0.944
41DAP/39DAP	1.06648	0.758
42DAP/41DAP	1.02247	1
43DAP/42DAP	1.07716	0.993
47DAP/43DAP	0.81444	0.424
52DAP/47DAP	1.01462	0.924
57DAP/52DAP	1.17493	0.948

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20889
17DAP/reference	0.65606	0.031
27DAP/reference	1.29631
39DAP/reference	0.63027	0.261
41DAP/reference	0.82401
42DAP/reference	0.88848	0.337
43DAP/reference	0.51712	0.067
47DAP/reference	1.05814	0.674
52DAP/reference	0.90857	0.283
57DAP/reference	0.64021

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95319	0.613
27DAP/17DAP	1.0743	0.747
39DAP/27DAP	0.93376	0.496
41DAP/39DAP	1.23115	0.469
42DAP/41DAP	1.05972	0.622
43DAP/42DAP	1.18945	0.134
47DAP/43DAP	1.06118	0.758
52DAP/47DAP	0.82534	0.161
57DAP/52DAP	1.15595	0.366
57DAP/7DAP	0.87647	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91412	0.138
17DAP/reference	1.22626	1
27DAP/reference	0.99803	0.614
39DAP/reference	1.4475	0.133
41DAP/reference	1.67526	0.013
42DAP/reference	1.45652	0.233
43DAP/reference	0.90708	0.266
47DAP/reference	0.89944	0.504
52DAP/reference	0.87607	0.213
57DAP/reference	1.12835	0.125

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.59496
17DAP/reference	1.07784	0.805
27DAP/reference	1.35335	0.67
39DAP/reference	0.84831	0.122
41DAP/reference	1.10934	0.525
42DAP/reference	1.11729	0.969
43DAP/reference	0.94379	0.552
47DAP/reference	0.77658	0.061
52DAP/reference	0.69356	0.016
57DAP/reference	0.68185	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94715	0.422
17DAP/reference	0.75508	0.358
27DAP/reference	1.51874	0.12
39DAP/reference	1.0029	0.819
41DAP/reference	1.98671	0.222
42DAP/reference	0.94957	0.671
43DAP/reference	1.0344	0.685
47DAP/reference	1.00857	0.754
52DAP/reference	1.11325	0.623
57DAP/reference	0.99049	0.704

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99037	1
26DAP/20DAP	1.07882	0.727
34DAP/26DAP	1.00944	1
51DAP/34DAP	1.34176	0.185
52DAP/51DAP	0.94882	1
53DAP/52DAP	1.23341	0.149
55DAP/53DAP	0.99475	0.908
57DAP/55DAP	1.16524	0.764
62DAP/57DAP	0.98455	0.994
68DAP/62DAP	0.96253	0.834
68DAP/14DAP	0.70673

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.74004	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.65869	0.027
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.73613
Mature Eggplant/Ripe Tomato	2.06947	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.89553
1-1-2/M82	1.25292
12-2/M82	0.79365
12-4/M82	1.00344
1-3/M82	N/A	N/A
2-1-1/M82	0.6766
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.95523
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.41784
4-3/M82	1.48095
5-3/M82	1.09105	0.572
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	1.14898	0.741
7-2/M82	1.17021
9-3-2/M82	1.51015

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.82414	0.321
IL2-6/WTpooled	0.87779	0.348
IL7-5/WTpooled	1.18129	0.792
IL7-3/WTpooled	0.82224	0.418
IL12-4/WTpooled	0.93171	0.71
IL1-4/WTpooled	0.95698	0.834
WT/WTpooled	0.93972	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	1.08194	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01496	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.98881
DC3000/delta hrp 24h	0.61763	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.05895	0.408
DC3000 delta B/DC3000 delta AB	1.15961	0.226

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00008	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.8397	0.338
Var 12h NI row2-row1	1.22409	1
Var 36h I row2-row1	1.27785	0.489
Var 36h NI row2-row1	1.62873	1
Var 60h I row2-row1	0.91405	0.832
Var 60h NI row2-row1	0.79077	0.292
Time course 0hI-0hNI	1.01848	1
Time course 12hI-12hNI	1.01683	0.816
Time course 36hI-36hNI	1.30127	0.006
Time course 60hI-60hNI	2.03734	0.008

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)	0.74603	0.485
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.95813	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90801	0.313

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)	0.89019	1
Manapal/WT (red)	1.55829	0.126