Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.16.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0554	0.964
27DAP/17DAP	0.82823	0.615
39DAP/27DAP	2.00733	0.025
41DAP/39DAP	0.76522	0.191
42DAP/41DAP	0.95308	1
43DAP/42DAP	1.04552	0.937
47DAP/43DAP	0.52262	0.053
52DAP/47DAP	1.27363	0.873
57DAP/52DAP	1.03814	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09482	0.421
17DAP/reference	1.12758	0.036
27DAP/reference	1.03388	0.435
39DAP/reference	1.0164	0.639
41DAP/reference	1.11069	0.073
42DAP/reference	0.92372	0.095
43DAP/reference	1.00911	1
47DAP/reference	0.89746	0.015
52DAP/reference	0.76689	0.021
57DAP/reference	0.8131	0.045

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92674	0.509
27DAP/17DAP	1.12492	0.5
39DAP/27DAP	0.85925	0.134
41DAP/39DAP	1.35989	0.214
42DAP/41DAP	1.08187	0.753
43DAP/42DAP	1.02179	1
47DAP/43DAP	0.97277	0.877
52DAP/47DAP	0.85139	0.439
57DAP/52DAP	1.14864	0.571
57DAP/7DAP	0.79789	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1639	0.087
17DAP/reference	1.00751	1
27DAP/reference	1.43373	0.01
39DAP/reference	1.68984	0.005
41DAP/reference	2.40991	0.009
42DAP/reference	2.0332	0.006
43DAP/reference	1.76866	0.007
47DAP/reference	1.50497	0.016
52DAP/reference	1.68856	0.007
57DAP/reference	1.68836	0.007

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00098	0.97
17DAP/reference	0.9769	0.461
27DAP/reference	0.92782	0.393
39DAP/reference	1.02894	1
41DAP/reference	1.12705	0.204
42DAP/reference	1.05468	0.488
43DAP/reference	1.07561	0.352
47DAP/reference	1.08394	0.124
52DAP/reference	0.96674	0.28
57DAP/reference	1.02458	0.755

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9091	0.158
17DAP/reference	0.93252	0.342
27DAP/reference	1.22642	0.425
39DAP/reference	1.37727	0.024
41DAP/reference	1.22843	0.035
42DAP/reference	1.18469	0.189
43DAP/reference	0.98549	0.639
47DAP/reference	0.99715	0.667
52DAP/reference	0.90904	0.395
57DAP/reference	0.853	0.065

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09961	0.966
26DAP/20DAP	1.92415	0.19
34DAP/26DAP	1.00959	0.998
51DAP/34DAP	1.73349	0.07
52DAP/51DAP	0.93009	1
53DAP/52DAP	1.35584	0.221
55DAP/53DAP	0.81038	0.042
57DAP/55DAP	1.13044	0.841
62DAP/57DAP	0.84945	0.466
68DAP/62DAP	0.68128	0.211
68DAP/14DAP	0.58397	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.70043	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.71497	0.194
Mature Green Tomato/Ripe Tomato	1.21727	0.299
Immature Eggplant/Mature Eggplant	0.94986	0.651
Ripe Pepper/Ripe Tomato	2.07922	1
Mature Eggplant/Ripe Tomato	0.78259	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.71647
12-2/M82	0.84414	0.496
12-4/M82	0.68678	0.319
1-3/M82	N/A	N/A
2-1-1/M82	0.88735	0.92
2-1/M82	0.66633
2-6/M82	1.23507
3-2/M82	0.99584	1
4-1-1/M82	1.03871
4-1/M82	N/A	N/A
4-3-2/M82	1.1976
4-3/M82	0.84485	0.551
5-3/M82	1.12994	1
6-2/M82	1.37472	0.198
6-3/M82	0.93483	1
7-1/M82	0.85171	0.803
7-2/M82	1.145
9-3-2/M82	1.25786	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.85251
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78431
IL12-4/WTpooled	1.22567	0.367
IL1-4/WTpooled	1.00529
WT/WTpooled	1.08899	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	1.22088	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99301	1
DC3000/delta hrp 6h	1.09791	0.95
DC3000/delta hrp 12h	1.10216	1
DC3000/delta hrp 24h	0.96405	0.831

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17453	0.254
Exp 36h	1.02342	1
Exp 60h	1.06847	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06762	1
Var 0h	0.94781	1
Var 12h I row2-row1	1.03301	1
Var 12h NI row2-row1	1.06959	1
Var 36h I row2-row1	1.2768	0.305
Var 36h NI row2-row1	0.67128	0.584
Var 60h I row2-row1	0.94061	0.952
Var 60h NI row2-row1	0.8834	0.572
Time course 0hI-0hNI	1.16653	0.719
Time course 12hI-12hNI	0.95536	0.742
Time course 36hI-36hNI	1.15151	0.025
Time course 60hI-60hNI	2.25147	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)	1.06571	0.541
transgenic ySAMdc/azygous control (breaker)	0.82244	0.173
transgenic ySAMdc/azygous control (red)	0.83631	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02673	0.448

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78655	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.85649	1
Manapal/WT (break)	1.02057	1
Manapal/WT (red)	0.9454	0.728