Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.1.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90989	0.586
27DAP/17DAP	0.95304	0.923
39DAP/27DAP	1.00487	0.798
41DAP/39DAP	0.87088	0.54
42DAP/41DAP	1.34357	0.419
43DAP/42DAP	1.03318	1
47DAP/43DAP	0.92048	0.696
52DAP/47DAP	0.94444	0.779
57DAP/52DAP	1.09155	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90608	0.238
17DAP/reference	0.84987	0.029
27DAP/reference	1.09609	0.348
39DAP/reference	0.83811	0.048
41DAP/reference	0.76895	0.031
42DAP/reference	0.90354	0.037
43DAP/reference	1.12906	0.025
47DAP/reference	0.9662	0.366
52DAP/reference	1.23729	0.035
57DAP/reference	1.36925	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16833	0.414
27DAP/17DAP	0.87819	0.172
39DAP/27DAP	1.01792	1
41DAP/39DAP	1.07596	0.774
42DAP/41DAP	0.98779	0.768
43DAP/42DAP	1.07906	1
47DAP/43DAP	0.86058	0.28
52DAP/47DAP	0.77574	0.142
57DAP/52DAP	1.12222	0.596
57DAP/7DAP	0.52678

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88297	0.146
17DAP/reference	1.05966	0.437
27DAP/reference	0.93885	0.185
39DAP/reference	1.07376	0.511
41DAP/reference	1.01943	0.864
42DAP/reference	1.05889	0.889
43DAP/reference	0.82417	0.037
47DAP/reference	1.09263	0.761
52DAP/reference	0.95304	0.363
57DAP/reference	1.0141	0.831

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91376	0.487
17DAP/reference	0.81486	0.109
27DAP/reference	0.98327	0.598
39DAP/reference	0.93527	0.442
41DAP/reference	1.2245	0.065
42DAP/reference	0.92397	0.237
43DAP/reference	0.80483	0.095
47DAP/reference	0.93736	0.24
52DAP/reference	0.88525	0.259
57DAP/reference	0.96395	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94641	0.362
17DAP/reference	0.94031	0.452
27DAP/reference	0.80641	0.035
39DAP/reference	0.90448	0.083
41DAP/reference	0.95574	0.512
42DAP/reference	1.04117	0.943
43DAP/reference	0.97021	0.523
47DAP/reference	0.92957	0.315
52DAP/reference	0.77969	0.193
57DAP/reference	1.9194	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.17927	0.966
26DAP/20DAP	1.32472	0.305
34DAP/26DAP	1.38763	0.542
51DAP/34DAP	1.56726	0.654
52DAP/51DAP	1.04359	1
53DAP/52DAP	0.69496	0.049
55DAP/53DAP	0.80887	0.062
57DAP/55DAP	0.5964	0.068
62DAP/57DAP	1.76859	0.445
68DAP/62DAP	2.0366	0.019
68DAP/14DAP	2.13293	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.68382	0.062

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.8809	0.058
Mature Green Tomato/Ripe Tomato	0.88003	0.446
Immature Eggplant/Mature Eggplant	0.45621	0.084
Ripe Pepper/Ripe Tomato	1.01818	1
Mature Eggplant/Ripe Tomato	0.62452	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.69409
12-2/M82	N/A	N/A
12-4/M82	0.83492	0.257
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	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.02581	1
6-2/M82	N/A	N/A
6-3/M82	1.0725
7-1/M82	N/A	N/A
7-2/M82	1.1239
9-3-2/M82	1.00811

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.93788	1
IL2-6/WTpooled	1.08346	0.46
IL7-5/WTpooled	0.86316	0.559
IL7-3/WTpooled	0.89911	0.418
IL12-4/WTpooled	1.09316	0.839
IL1-4/WTpooled	1.05768	1
WT/WTpooled	1.09458	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	0.78649	0.497

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89571	0.839
DC3000/delta hrp 6h	1.01319	0.95
DC3000/delta hrp 12h	1.07796	1
DC3000/delta hrp 24h	0.74725	0.044

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65421	0.041
DC3000 delta B/DC3000 delta AB	0.62735	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99648	1
Exp 36h	0.88707	0.589
Exp 60h	0.86594	0.454

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98844	1
Var 0h	0.90512	0.933
Var 12h I row2-row1	0.84138	0.467
Var 12h NI row2-row1	0.99435	1
Var 36h I row2-row1	0.93746	1
Var 36h NI row2-row1	1.22358	0.482
Var 60h I row2-row1	0.9199	0.832
Var 60h NI row2-row1	1.29814	0.904
Time course 0hI-0hNI	0.93842	0.649
Time course 12hI-12hNI	0.95688	0.746
Time course 36hI-36hNI	0.8613	0.073
Time course 60hI-60hNI	0.19731	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)	0.99946	1
transgenic ySAMdc/azygous control (breaker)	0.99835	1
transgenic ySAMdc/azygous control (red)	1.05778	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04241	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05634	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.05073	0.307
Manapal/WT (break)	0.96847	1
Manapal/WT (red)	0.92409	0.242