Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.20.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05556	0.927
27DAP/17DAP	1.26375	0.772
39DAP/27DAP	1.37284	0.798
41DAP/39DAP	1.50259	0.289
42DAP/41DAP	1.05044	1
43DAP/42DAP	0.97683	0.914
47DAP/43DAP	0.95164	0.744
52DAP/47DAP	1.36337	0.372
57DAP/52DAP	0.86869	0.827

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77446	0.051
17DAP/reference	0.77454	0.009
27DAP/reference	0.75057	0.014
39DAP/reference	0.77811	0.012
41DAP/reference	0.73487	0.018
42DAP/reference	0.83641	0.006
43DAP/reference	0.89172	0.08
47DAP/reference	0.93027	0.174
52DAP/reference	1.1384	0.229
57DAP/reference	1.17759	0.012

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42423	0.445
27DAP/17DAP	0.86909	0.782
39DAP/27DAP	1.09522	0.553
41DAP/39DAP	1.1546	0.849
42DAP/41DAP	0.96722	0.674
43DAP/42DAP	1.39221	0.147
47DAP/43DAP	0.85444	0.597
52DAP/47DAP	1.20669	0.524
57DAP/52DAP	1.95659	0.042
57DAP/7DAP	1.82487

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82601	0.082
17DAP/reference	0.8702	0.035
27DAP/reference	0.9398	0.231
39DAP/reference	0.78576	0.043
41DAP/reference	0.64068	0.021
42DAP/reference	0.7761	0.02
43DAP/reference	0.83267	0.059
47DAP/reference	0.99282	1
52DAP/reference	0.93734	0.304
57DAP/reference	0.77358	0.017

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.61604	0.011
17DAP/reference	0.68161	0.005
27DAP/reference	1.48465	1
39DAP/reference	0.88626	0.108
41DAP/reference	0.86636	0.105
42DAP/reference	0.91975	0.189
43DAP/reference	0.85602	0.229
47DAP/reference	0.81602	0.014
52DAP/reference	0.88132	0.111
57DAP/reference	0.63322	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84558	0.055
17DAP/reference	0.85436	0.125
27DAP/reference	0.86089	0.089
39DAP/reference	0.95985	0.43
41DAP/reference	1.12582	0.411
42DAP/reference	1.08478	0.459
43DAP/reference	1.09269	0.412
47DAP/reference	0.97298	0.434
52DAP/reference	0.81417	0.134
57DAP/reference	1.23023	0.046

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.35826	0.878
26DAP/20DAP	0.95485	1
34DAP/26DAP	4.92222	0.819
51DAP/34DAP	0.9306
52DAP/51DAP	1.52741	0.246
53DAP/52DAP	1.01197	0.901
55DAP/53DAP	1.2259	0.741
57DAP/55DAP	0.75193	0.12
62DAP/57DAP	1.21343	0.767
68DAP/62DAP	2.0495	0.03
68DAP/14DAP	1.7886	0.091

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.72802	0.155

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.72763	0.182
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.60386	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.81137
12-2/M82	N/A	N/A
12-4/M82	0.90217	1
1-3/M82	N/A	N/A
2-1-1/M82	0.40622
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.05445
4-1-1/M82	N/A	N/A
4-1/M82	0.40148	1
4-3-2/M82	0.76241	0.698
4-3/M82	0.69175
5-3/M82	0.93013
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.68907
9-3-2/M82	0.74003	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06851	0.493
IL2-6/WTpooled	0.83483	0.473
IL7-5/WTpooled	1.12625	1
IL7-3/WTpooled	0.98751	1
IL12-4/WTpooled	0.82805	0.71
IL1-4/WTpooled	0.92854	0.834
WT/WTpooled	1.0284	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	1.00055

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.87604	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.18503	1
DC3000/delta hrp 24h	1.10177	0.383

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	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	N/A	N/A
Var 12h I row2-row1	0.85881
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	2.07114
Var 60h I row2-row1	1.67547
Var 60h NI row2-row1	0.57576	1
Time course 0hI-0hNI	1.36754	0.719
Time course 12hI-12hNI	1.20511	0.227
Time course 36hI-36hNI	1.36162	0.881
Time course 60hI-60hNI	1.13621

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)	0.97351	0.789
transgenic ySAMdc/azygous control (breaker)	1.11769	1
transgenic ySAMdc/azygous control (red)	0.94	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00638	0.854

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94314	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83447	1
Manapal/WT (break)	1.01446	1
Manapal/WT (red)	1.13843	0.222