Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96497	0.77
27DAP/17DAP	1.07648	0.92
39DAP/27DAP	0.74303	0.392
41DAP/39DAP	1.53793	0.359
42DAP/41DAP	1.0149	1
43DAP/42DAP	0.84618	0.467
47DAP/43DAP	0.98827	0.904
52DAP/47DAP	1.59223	0.281
57DAP/52DAP	0.95493	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04096	0.71
17DAP/reference	0.97138	0.169
27DAP/reference	0.99388	0.779
39DAP/reference	1.01376	0.393
41DAP/reference	0.99779	1
42DAP/reference	0.95248	0.043
43DAP/reference	0.99639	0.882
47DAP/reference	0.90654	0.004
52DAP/reference	0.98962	0.598
57DAP/reference	0.8656	0.031

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99645	0.871
27DAP/17DAP	0.99636	0.943
39DAP/27DAP	1.00322	1
41DAP/39DAP	1.04592	0.876
42DAP/41DAP	1.02307	0.893
43DAP/42DAP	0.94658	0.28
47DAP/43DAP	1.0113	0.897
52DAP/47DAP	0.9855	0.917
57DAP/52DAP	1.01039	0.997
57DAP/7DAP	1.07949	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91972	0.078
17DAP/reference	0.97954	0.044
27DAP/reference	0.93428	0.022
39DAP/reference	0.98156	0.354
41DAP/reference	0.95318	0.213
42DAP/reference	1.02531	0.405
43DAP/reference	0.99305	0.637
47DAP/reference	0.95485	0.293
52DAP/reference	0.92911	0.137
57DAP/reference	0.98171	0.443

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99593	0.907
17DAP/reference	1.01545	0.806
27DAP/reference	0.95672	0.327
39DAP/reference	0.93624	0.136
41DAP/reference	0.97516	0.451
42DAP/reference	0.95441	0.355
43DAP/reference	0.98146	0.633
47DAP/reference	0.99755	0.73
52DAP/reference	0.95516	0.239
57DAP/reference	1.00846	0.868

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94267	0.135
17DAP/reference	0.96501	0.374
27DAP/reference	0.97839	0.218
39DAP/reference	1.01949	0.65
41DAP/reference	0.95996	0.025
42DAP/reference	0.97287	0.445
43DAP/reference	0.9441	0.15
47DAP/reference	0.94992	0.24
52DAP/reference	1.00205	0.928
57DAP/reference	0.87503	0.074

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94637	0.981
26DAP/20DAP	0.95254	1
34DAP/26DAP	0.97742	0.936
51DAP/34DAP	0.90742	0.286
52DAP/51DAP	1.01573	0.77
53DAP/52DAP	1.04666	0.797
55DAP/53DAP	1.00547	0.951
57DAP/55DAP	1.01191	1
62DAP/57DAP	0.98799	0.994
68DAP/62DAP	0.99191	0.885
68DAP/14DAP	0.80303	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96503	0.422

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.78011	0.047
Immature Eggplant/Mature Eggplant	1.64718	0.05
Ripe Pepper/Ripe Tomato	1.79577
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.07448	1
1-1-2/M82	0.95589	0.754
12-2/M82	1.00154	1
12-4/M82	1.01274	1
1-3/M82	0.9612	1
2-1-1/M82	0.99534	1
2-1/M82	N/A	N/A
2-6/M82	0.99434	1
3-2/M82	1.00306	1
4-1-1/M82	0.97056	1
4-1/M82	0.99981	1
4-3-2/M82	0.84103	0.698
4-3/M82	0.97223	1
5-3/M82	0.97637	1
6-2/M82	1.03246	0.253
6-3/M82	1.04772	1
7-1/M82	0.91514	0.803
7-2/M82	1.03447	1
9-3-2/M82	0.97289	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.16642	0.531
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08186	1
IL12-4/WTpooled	1.04449	0.737
IL1-4/WTpooled	0.96806
WT/WTpooled	1.0221	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	1.20381	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05654	0.875
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.0957	1
DC3000/delta hrp 24h	1.00937	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.0266	0.408
DC3000 delta B/DC3000 delta AB	1.0734	0.398

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	1.188	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99447	1
Var 0h	1.09157	0.782
Var 12h I row2-row1	1.19878	0.198
Var 12h NI row2-row1	0.9684	0.906
Var 36h I row2-row1	0.96605	1
Var 36h NI row2-row1	0.91418	0.645
Var 60h I row2-row1	1.19691	0.562
Var 60h NI row2-row1	1.11975	0.904
Time course 0hI-0hNI	1.07171	0.852
Time course 12hI-12hNI	1.02957	0.827
Time course 36hI-36hNI	1.00969	0.881
Time course 60hI-60hNI	1.27283	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)	1.35311	0.238
transgenic ySAMdc/azygous control (breaker)	0.94872	1
transgenic ySAMdc/azygous control (red)	1.22172	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04111	0.17

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01402	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00649	1
Manapal/WT (break)	0.86048	1
Manapal/WT (red)	0.54322	0.181