Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.2.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76702	0.067
27DAP/17DAP	0.72471	0.293
39DAP/27DAP	0.62759	0.293
41DAP/39DAP	0.55746	0.041
42DAP/41DAP	0.85592	0.774
43DAP/42DAP	1.59032	0.07
47DAP/43DAP	0.969	0.864
52DAP/47DAP	0.63878	0.185
57DAP/52DAP	0.81621	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.31301	0.105
17DAP/reference	1.18923	0.03
27DAP/reference	1.252	0.02
39DAP/reference	0.91967	0.267
41DAP/reference	0.91145	0.267
42DAP/reference	0.88022	0.021
43DAP/reference	0.8617	0.084
47DAP/reference	0.79142	0.002
52DAP/reference	0.82073	0.024
57DAP/reference	0.811	0.019

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97462	0.697
27DAP/17DAP	1.0268	0.942
39DAP/27DAP	0.57532	0.031
41DAP/39DAP	0.56814	0.013
42DAP/41DAP	0.97205	0.737
43DAP/42DAP	0.92808	0.447
47DAP/43DAP	0.8154	0.056
52DAP/47DAP	0.89889	0.612
57DAP/52DAP	1.11471	0.654
57DAP/7DAP	0.28555	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.18017	0.024
17DAP/reference	1.32129	0.026
27DAP/reference	1.10763	0.301
39DAP/reference	0.83444	0.073
41DAP/reference	0.93602	0.166
42DAP/reference	1.01532	0.889
43DAP/reference	0.92241	0.202
47DAP/reference	0.90286	0.128
52DAP/reference	0.8843	0.115
57DAP/reference	0.93355	0.097

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18636	0.545
17DAP/reference	1.32391	0.011
27DAP/reference	1.18877	0.373
39DAP/reference	0.76066	0.033
41DAP/reference	1.03534	0.752
42DAP/reference	0.90879	0.169
43DAP/reference	0.69935	0.017
47DAP/reference	0.79391	0.012
52DAP/reference	0.719	0.005
57DAP/reference	0.67573	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.00579	0.015
17DAP/reference	1.50868	0.157
27DAP/reference	1.44074	0.02
39DAP/reference	0.98391	0.591
41DAP/reference	0.9717	0.512
42DAP/reference	0.7658	0.017
43DAP/reference	0.78643	0.043
47DAP/reference	0.73556	0.005
52DAP/reference	0.97914	0.663
57DAP/reference	0.70694	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06698	0.966
26DAP/20DAP	1.16596	0.663
34DAP/26DAP	1.03096	1
51DAP/34DAP	1.99483	0.032
52DAP/51DAP	0.82221	1
53DAP/52DAP	1.54159	0.045
55DAP/53DAP	0.90107	0.5
57DAP/55DAP	0.86262	0.41
62DAP/57DAP	0.74717	0.088
68DAP/62DAP	1.11343	0.788
68DAP/14DAP	1.52906	0.059

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.26985	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.57725	0.118
Mature Green Tomato/Ripe Tomato	5.29703	0.015
Immature Eggplant/Mature Eggplant	0.45911	0.057
Ripe Pepper/Ripe Tomato	21.4327	0.258
Mature Eggplant/Ripe Tomato	10.862	0.26

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	0.687
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	1.60376
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	2.10905

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.09092	0.46
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08939	1
IL12-4/WTpooled	1.13994	0.595
IL1-4/WTpooled	0.87705
WT/WTpooled	0.95235	0.764

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	0.8993	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01881	0.921
DC3000/delta hrp 6h	0.9487	0.95
DC3000/delta hrp 12h	0.92245	1
DC3000/delta hrp 24h	0.43618	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.66791	0.085
DC3000 delta B/DC3000 delta AB	0.57011	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04123	1
Exp 36h	0.85206	0.449
Exp 60h	0.77445	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01056	1
Var 0h	1.09524	1
Var 12h I row2-row1	0.86152	0.344
Var 12h NI row2-row1	1.03706	1
Var 36h I row2-row1	1.01803	1
Var 36h NI row2-row1	1.12825	0.482
Var 60h I row2-row1	1.15062	0.543
Var 60h NI row2-row1	1.02668	1
Time course 0hI-0hNI	0.97444	0.892
Time course 12hI-12hNI	0.94514	0.668
Time course 36hI-36hNI	0.82668	0.025
Time course 60hI-60hNI	0.14951	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)	0.73202	0.285
transgenic ySAMdc/azygous control (breaker)	1.03828	1
transgenic ySAMdc/azygous control (red)	1.20948	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89173	0.105

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	3.03463	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.49925	0.09
Manapal/WT (break)	1.08505	1
Manapal/WT (red)	1.19607	1