Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.20.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07351	0.964
27DAP/17DAP	0.9723	0.966
39DAP/27DAP	0.68569	0.495
41DAP/39DAP	2.12532	0.398
42DAP/41DAP	1.22649	0.967
43DAP/42DAP	0.98333	0.93
47DAP/43DAP	0.83311	0.487
52DAP/47DAP	1.86579	0.306
57DAP/52DAP	0.83675	0.765

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88184	0.136
17DAP/reference	0.99311	0.858
27DAP/reference	0.98774	0.711
39DAP/reference	0.98298	0.75
41DAP/reference	0.99803	1
42DAP/reference	0.90242	0.032
43DAP/reference	1.06611	0.495
47DAP/reference	0.91173	0.011
52DAP/reference	0.89935	0.147
57DAP/reference	0.86085	0.03

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03288	0.934
27DAP/17DAP	0.92302	0.363
39DAP/27DAP	1.04295	0.581
41DAP/39DAP	1.06233	0.837
42DAP/41DAP	0.97913	0.776
43DAP/42DAP	1.00378	1
47DAP/43DAP	0.9817	0.919
52DAP/47DAP	0.97949	0.905
57DAP/52DAP	1.01439	0.984
57DAP/7DAP	0.98647	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51391	0.062
17DAP/reference	2.14685	0.006
27DAP/reference	2.06153	0.006
39DAP/reference	2.36426	0.005
41DAP/reference	2.63655	0.01
42DAP/reference	3.01978	0.006
43DAP/reference	2.99065	0.006
47DAP/reference	1.7233	0.311
52DAP/reference	2.44842	0.007
57DAP/reference	2.24872	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97867	0.736
17DAP/reference	0.86524	0.062
27DAP/reference	0.83296	0.134
39DAP/reference	0.81121	0.054
41DAP/reference	0.75828	0.031
42DAP/reference	0.80306	0.013
43DAP/reference	0.85329	0.243
47DAP/reference	0.78595	0.016
52DAP/reference	0.88815	0.009
57DAP/reference	0.9581	0.433

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77331	0.02
17DAP/reference	1.16063	0.558
27DAP/reference	1.71804	0.025
39DAP/reference	1.6149	0.017
41DAP/reference	1.76723	0.008
42DAP/reference	1.56981	0.082
43DAP/reference	1.53201	0.32
47DAP/reference	0.94446	0.325
52DAP/reference	2.04642	0.087
57DAP/reference	1.12928	0.633

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.8615	0.672
26DAP/20DAP	0.88324	0.512
34DAP/26DAP	0.93745	0.642
51DAP/34DAP	1.01917	0.925
52DAP/51DAP	0.90067	1
53DAP/52DAP	1.06701	0.806
55DAP/53DAP	1.01327	0.951
57DAP/55DAP	1.0627	0.927
62DAP/57DAP	1.38838	0.081
68DAP/62DAP	1.01969	0.81
68DAP/14DAP	1.1738	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.87188	0.068

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.91809	0.446
Immature Eggplant/Mature Eggplant	2.25237	0.136
Ripe Pepper/Ripe Tomato	0.92692	1
Mature Eggplant/Ripe Tomato	0.67891	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.9459	0.944
1-1-2/M82	0.79319	0.804
12-2/M82	1.03767
12-4/M82	1.02052	1
1-3/M82	0.78375	0.378
2-1-1/M82	1.1314
2-1/M82	N/A	N/A
2-6/M82	0.96009	1
3-2/M82	N/A	N/A
4-1-1/M82	0.71623
4-1/M82	0.78518	1
4-3-2/M82	0.95028
4-3/M82	0.66353	0.611
5-3/M82	0.95568	1
6-2/M82	0.82946
6-3/M82	0.92341
7-1/M82	N/A	N/A
7-2/M82	1.00374	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.54424	0.277
IL2-6/WTpooled	0.77736	1
IL7-5/WTpooled	1.04711	1
IL7-3/WTpooled	1.75428	0.362
IL12-4/WTpooled	1.07598	0.673
IL1-4/WTpooled	1.1648	1
WT/WTpooled	1.08608	0.87

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	1.02877	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99419	1
DC3000/delta hrp 6h	0.84771	0.95
DC3000/delta hrp 12h	0.50708
DC3000/delta hrp 24h	1.22164	0.107

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16993	0.208
DC3000 delta B/DC3000 delta AB	1.08042	0.516

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	2.71593	0.489
Exp 60h	2.64491	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03014	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.0981	0.283
Var 12h NI row2-row1	1.14303	1
Var 36h I row2-row1	0.94357	1
Var 36h NI row2-row1	0.8409	0.469
Var 60h I row2-row1	1.11117	0.562
Var 60h NI row2-row1	1.16939	0.904
Time course 0hI-0hNI	1.09486	0.799
Time course 12hI-12hNI	1.2497	0.046
Time course 36hI-36hNI	1.30769	0.01
Time course 60hI-60hNI	1.79947	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)	3.22551	0.397
transgenic ySAMdc/azygous control (breaker)	0.90903	0.49
transgenic ySAMdc/azygous control (red)	2.91521	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01055	0.723

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91558	0.431

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)	N/A	N/A
Manapal/WT (red)	0.67686	0.315