Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.8.3

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85172	0.339
27DAP/17DAP	0.84641	0.593
39DAP/27DAP	1.13586	0.685
41DAP/39DAP	0.85136	0.436
42DAP/41DAP	0.93479	1
43DAP/42DAP	0.99304	0.937
47DAP/43DAP	0.86406	0.565
52DAP/47DAP	1.29032	0.729
57DAP/52DAP	0.87357	0.727

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00513	0.844
17DAP/reference	0.90963	0.074
27DAP/reference	0.93034	0.304
39DAP/reference	1.24273	0.016
41DAP/reference	1.08449	0.073
42DAP/reference	0.95814	0.268
43DAP/reference	0.92602	0.107
47DAP/reference	0.94558	0.3
52DAP/reference	0.93682	0.267
57DAP/reference	1.03124	0.802

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99286	0.826
27DAP/17DAP	1.03451	0.887
39DAP/27DAP	0.93651	0.382
41DAP/39DAP	1.16983	0.497
42DAP/41DAP	0.94861	0.584
43DAP/42DAP	0.88284	0.101
47DAP/43DAP	0.99808	0.998
52DAP/47DAP	0.94018	0.702
57DAP/52DAP	0.93395	0.545
57DAP/7DAP	0.98862	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88073	0.27
17DAP/reference	1.12938	0.297
27DAP/reference	1.74709	0.009
39DAP/reference	0.8727	0.109
41DAP/reference	1.12799	0.303
42DAP/reference	1.32606	0.018
43DAP/reference	0.93474	0.21
47DAP/reference	1.06436	0.67
52DAP/reference	1.00921	0.74
57DAP/reference	0.90781	0.036

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.28565	0.049
17DAP/reference	1.29749	0.052
27DAP/reference	1.36144	0.054
39DAP/reference	1.28721	0.046
41DAP/reference	1.47241	0.005
42DAP/reference	1.58194	0.008
43DAP/reference	1.8278	0.061
47DAP/reference	1.66574	0.008
52DAP/reference	1.65837	0.009
57DAP/reference	1.26671	0.06

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9224	0.249
17DAP/reference	1.01426	1
27DAP/reference	0.93646	0.133
39DAP/reference	1.06739	0.365
41DAP/reference	1.2535	0.139
42DAP/reference	1.3959	0.02
43DAP/reference	0.87103	0.179
47DAP/reference	1.01936	1
52DAP/reference	1.13338	0.301
57DAP/reference	0.9818	0.623

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.09864	0.966
26DAP/20DAP	1.57613	0.099
34DAP/26DAP	0.96744	0.917
51DAP/34DAP	0.92201	0.537
52DAP/51DAP	1.16028	0.054
53DAP/52DAP	0.89969	0.52
55DAP/53DAP	0.82369	0.023
57DAP/55DAP	1.07298	0.955
62DAP/57DAP	1.20662	0.833
68DAP/62DAP	1.22061	0.831
68DAP/14DAP	1.01703	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18603	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.15561	0.058
Mature Green Tomato/Ripe Tomato	1.37237	0.024
Immature Eggplant/Mature Eggplant	1.16367	0.053
Ripe Pepper/Ripe Tomato	1.50958	1
Mature Eggplant/Ripe Tomato	3.50931	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.30336	0.418
1-1-2/M82	1.05306	1
12-2/M82	0.79087
12-4/M82	0.97243	1
1-3/M82	1.04854
2-1-1/M82	1.33766
2-1/M82	N/A	N/A
2-6/M82	1.13805	0.425
3-2/M82	1.0884	0.967
4-1-1/M82	1.38645	0.968
4-1/M82	1.2298
4-3-2/M82	1.46487	0.253
4-3/M82	1.36675	1
5-3/M82	0.91294	1
6-2/M82	1.01451
6-3/M82	1.11825
7-1/M82	N/A	N/A
7-2/M82	1.1562
9-3-2/M82	1.33425	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.99911	1
IL7-5/WTpooled	0.7565
IL7-3/WTpooled	0.90779	0.418
IL12-4/WTpooled	0.79826	0.581
IL1-4/WTpooled	1.03054	1
WT/WTpooled	0.91105	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	1.09903	0.479

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02801	0.921
DC3000/delta hrp 6h	1.12768	1
DC3000/delta hrp 12h	1.01014	1
DC3000/delta hrp 24h	0.99838	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1835	0.042
DC3000 delta B/DC3000 delta AB	1.05813	0.491

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99798	1
Exp 36h	1.19125	0.693
Exp 60h	1.04069	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00194	1
Var 0h	0.59954	0.457
Var 12h I row2-row1	0.98652	1
Var 12h NI row2-row1	1.12783	0.649
Var 36h I row2-row1	0.9603	1
Var 36h NI row2-row1	1.00749	1
Var 60h I row2-row1	0.84933	0.582
Var 60h NI row2-row1	0.84259	0.302
Time course 0hI-0hNI	0.94289	0.675
Time course 12hI-12hNI	1.07464	0.367
Time course 36hI-36hNI	1.37028	0.017
Time course 60hI-60hNI	1.76284	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)	0.9314	0.309
transgenic ySAMdc/azygous control (breaker)	0.63627	0.173
transgenic ySAMdc/azygous control (red)	0.89797	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.07729	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.44629	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.69481	0.172
Manapal/WT (break)	0.94494	1
Manapal/WT (red)	0.6392	0.274