Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.14.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70429	0.089
27DAP/17DAP	0.79009	0.52
39DAP/27DAP	1.60587	0.105
41DAP/39DAP	0.71657	0.147
42DAP/41DAP	0.98544	1
43DAP/42DAP	1.20734	0.968
47DAP/43DAP	0.41372	0.049
52DAP/47DAP	1.05977	0.92
57DAP/52DAP	1.52335	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.85181	0.007
17DAP/reference	1.05723	0.737
27DAP/reference	0.67499	0.02
39DAP/reference	0.72526	0.054
41DAP/reference	0.71204	0.049
42DAP/reference	1.07486	0.352
43DAP/reference	0.79811	0.077
47DAP/reference	0.81712	0.005
52DAP/reference	0.54799	0.013
57DAP/reference	0.79217	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95383	0.56
27DAP/17DAP	1.03096	1
39DAP/27DAP	0.67541	0.031
41DAP/39DAP	1.40339	0.914
42DAP/41DAP	1.08138	1
43DAP/42DAP	0.8634	0.022
47DAP/43DAP	0.9325	0.617
52DAP/47DAP	0.56997	0.048
57DAP/52DAP	0.82806	0.43
57DAP/7DAP	0.24206	0.186

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	3.39111	0.024
17DAP/reference	2.20831	0.009
27DAP/reference	1.66402	0.008
39DAP/reference	1.46281	0.008
41DAP/reference	1.87166	0.008
42DAP/reference	1.95331	0.009
43DAP/reference	1.47097	0.008
47DAP/reference	1.22647	0.049
52DAP/reference	1.51678	0.034
57DAP/reference	1.20922	0.076

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.42818	0.269
17DAP/reference	1.59263	0.009
27DAP/reference	1.63377	0.04
39DAP/reference	0.94947	0.33
41DAP/reference	1.40181	0.005
42DAP/reference	1.58842	0.008
43DAP/reference	0.78514	0.114
47DAP/reference	1.1436	0.061
52DAP/reference	0.63241	0.003
57DAP/reference	0.67414	0.028

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.38576	0.015
17DAP/reference	1.61963	0.177
27DAP/reference	1.60437	0.023
39DAP/reference	1.67687	0.01
41DAP/reference	1.15109	0.089
42DAP/reference	1.12664	0.443
43DAP/reference	1.24151	0.19
47DAP/reference	0.5133	0.005
52DAP/reference	0.92831	0.334
57DAP/reference	0.91167	0.258

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.53357	0.159
26DAP/20DAP	3.9672	0.097
34DAP/26DAP	0.5758	0.084
51DAP/34DAP	0.81874	0.127
52DAP/51DAP	0.83301	0.151
53DAP/52DAP	1.06085	0.921
55DAP/53DAP	0.64933	0.06
57DAP/55DAP	1.22463	0.492
62DAP/57DAP	1.08647	0.767
68DAP/62DAP	1.04126	1
68DAP/14DAP	1.16142	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	5.02781	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.02618	0.666
Mature Green Tomato/Ripe Tomato	2.24624	0.015
Immature Eggplant/Mature Eggplant	1.06674	0.3
Ripe Pepper/Ripe Tomato	1.24053	1
Mature Eggplant/Ripe Tomato	1.27638	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.90605	0.841
1-1-2/M82	1.46854	0.977
12-2/M82	0.86423	0.955
12-4/M82	1.2118	1
1-3/M82	1.91426	0.277
2-1-1/M82	1.1342	1
2-1/M82	1.05215	1
2-6/M82	1.26516	0.425
3-2/M82	1.23338	0.549
4-1-1/M82	1.46985	1
4-1/M82	1.45558	1
4-3-2/M82	1.73824	0.508
4-3/M82	1.57164	1
5-3/M82	1.35614	0.572
6-2/M82	2.31339	0.222
6-3/M82	1.12086	1
7-1/M82	1.05938	1
7-2/M82	1.85627	0.302
9-3-2/M82	1.93332	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.0924
IL2-6/WTpooled	0.75384	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.2107	0.362
IL12-4/WTpooled	1.09333	0.673
IL1-4/WTpooled	0.95768	0.415
WT/WTpooled	0.97295	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	1.21294	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98024	1
DC3000/delta hrp 6h	0.98996	0.95
DC3000/delta hrp 12h	1.47048	1
DC3000/delta hrp 24h	1.20885	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24897	0.042
DC3000 delta B/DC3000 delta AB	1.50963	0.083

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.23285	1
Exp 36h	1.27842	0.693
Exp 60h	1.57069	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0037	1
Var 0h	0.52436	1
Var 12h I row2-row1	0.96096	0.856
Var 12h NI row2-row1	1.05479	1
Var 36h I row2-row1	1.21458	0.41
Var 36h NI row2-row1	0.83249	0.522
Var 60h I row2-row1	0.80411	0.285
Var 60h NI row2-row1	0.89696	0.69
Time course 0hI-0hNI	1.07616	0.603
Time course 12hI-12hNI	1.05899	0.633
Time course 36hI-36hNI	1.45291	0.005
Time course 60hI-60hNI	3.62383	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)	1.06206	0.798
transgenic ySAMdc/azygous control (breaker)	1.19024	1
transgenic ySAMdc/azygous control (red)	1.29479	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.30016	0.223

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05753	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00887	1
Manapal/WT (break)	1.04516	1
Manapal/WT (red)	0.88725	0.274