Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.19.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07752	0.919
27DAP/17DAP	1.07546	0.883
39DAP/27DAP	1.04815	0.927
41DAP/39DAP	0.99966	0.854
42DAP/41DAP	1.17798	0.958
43DAP/42DAP	1.02328	1
47DAP/43DAP	1.15176	0.563
52DAP/47DAP	1.10258	0.769
57DAP/52DAP	1.20794	0.92

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07014	0.097
17DAP/reference	1.09664	0.023
27DAP/reference	0.98487	0.725
39DAP/reference	0.97516	0.6
41DAP/reference	1.00563	1
42DAP/reference	1.00712	1
43DAP/reference	0.96395	0.331
47DAP/reference	0.95783	0.174
52DAP/reference	0.89961	0.037
57DAP/reference	0.82347	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99455	0.826
27DAP/17DAP	1.03961	0.909
39DAP/27DAP	1.13834	0.514
41DAP/39DAP	1.01725	1
42DAP/41DAP	0.98805	0.835
43DAP/42DAP	1.16891	0.034
47DAP/43DAP	1.14042	0.039
52DAP/47DAP	0.99659	0.97
57DAP/52DAP	1.05031	0.718
57DAP/7DAP	1.15776	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83324	0.104
17DAP/reference	0.84929	0.072
27DAP/reference	0.78104	0.01
39DAP/reference	0.84226	0.013
41DAP/reference	0.79218	0.017
42DAP/reference	0.78011	0.011
43DAP/reference	0.71173	0.02
47DAP/reference	0.90142	0.168
52DAP/reference	0.66259	0.012
57DAP/reference	0.74108	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96545	0.487
17DAP/reference	0.98558	0.561
27DAP/reference	0.95427	0.34
39DAP/reference	0.97359	0.469
41DAP/reference	0.78026	0.009
42DAP/reference	0.90963	0.073
43DAP/reference	0.96211	0.414
47DAP/reference	0.90852	0.032
52DAP/reference	0.88367	0.02
57DAP/reference	1.01645	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82004	0.032
17DAP/reference	0.86815	0.144
27DAP/reference	0.78731	0.026
39DAP/reference	0.77152	0.007
41DAP/reference	0.80562	0.02
42DAP/reference	0.77882	0.015
43DAP/reference	0.84317	0.024
47DAP/reference	0.83158	0.008
52DAP/reference	0.7016	0.082
57DAP/reference	0.73854	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9973	1
26DAP/20DAP	0.84688	0.244
34DAP/26DAP	1.11848	0.819
51DAP/34DAP	1.00902	0.988
52DAP/51DAP	1.13214	0.349
53DAP/52DAP	1.01209	1
55DAP/53DAP	1.12951	0.671
57DAP/55DAP	0.91849	0.664
62DAP/57DAP	1.01394	0.935
68DAP/62DAP	0.85254	0.263
68DAP/14DAP	0.94433	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.92713	0.341

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77314	0.228
Mature Green Tomato/Ripe Tomato	0.96904	0.66
Immature Eggplant/Mature Eggplant	1.10197	0.248
Ripe Pepper/Ripe Tomato	1.20146	0.258
Mature Eggplant/Ripe Tomato	0.42542	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0349	1
1-1-2/M82	0.90969	0.804
12-2/M82	1.12713	1
12-4/M82	0.94731	1
1-3/M82	1.05501	1
2-1-1/M82	0.93516	1
2-1/M82	0.79853	0.322
2-6/M82	1.20909	0.505
3-2/M82	N/A	N/A
4-1-1/M82	0.96878	1
4-1/M82	1.00144	1
4-3-2/M82	0.82773
4-3/M82	1.0855	0.268
5-3/M82	1.06118	0.572
6-2/M82	1.00432	1
6-3/M82	0.89165	1
7-1/M82	N/A	N/A
7-2/M82	1.09633	0.385
9-3-2/M82	0.69717

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.64098
IL7-5/WTpooled	0.88348
IL7-3/WTpooled	1.11125	1
IL12-4/WTpooled	1.19569	0.481
IL1-4/WTpooled	0.89551	0.834
WT/WTpooled	1.21101	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	0.87433	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03039	0.921
DC3000/delta hrp 6h	1.0811	1
DC3000/delta hrp 12h	0.95256	1
DC3000/delta hrp 24h	1.01752	0.797

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.09165	0.408
DC3000 delta B/DC3000 delta AB	1.07823	0.477

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96623	1
Exp 36h	1.12556	0.693
Exp 60h	1.17348	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97509	1
Var 0h	1.03945	1
Var 12h I row2-row1	1.07555	0.654
Var 12h NI row2-row1	0.89606	0.494
Var 36h I row2-row1	0.91132	0.805
Var 36h NI row2-row1	1.02339	1
Var 60h I row2-row1	1.17004	1
Var 60h NI row2-row1	1.11504	0.904
Time course 0hI-0hNI	1.00815	0.867
Time course 12hI-12hNI	0.9734	0.799
Time course 36hI-36hNI	0.95456	0.317
Time course 60hI-60hNI	0.96273	0.646

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)	1.06426	0.36
transgenic ySAMdc/azygous control (breaker)	0.74711	0.173
transgenic ySAMdc/azygous control (red)	0.84587	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01826	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.96681	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98514	1
Manapal/WT (break)	1.03438	1
Manapal/WT (red)	0.90494	0.36