Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-8.3.19.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97382	0.779
27DAP/17DAP	1.10893	1
39DAP/27DAP	0.96951	0.682
41DAP/39DAP	1.61896	0.27
42DAP/41DAP	0.97579	1
43DAP/42DAP	0.93878	0.883
47DAP/43DAP	1.01818	0.953
52DAP/47DAP	1.22829	0.521
57DAP/52DAP	0.89358	0.895

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22339	0.179
17DAP/reference	1.18124	0.089
27DAP/reference	1.10116	0.258
39DAP/reference	1.00011	0.991
41DAP/reference	1.29465	0.02
42DAP/reference	1.1603	0.007
43DAP/reference	1.15944	0.425
47DAP/reference	0.99004	0.535
52DAP/reference	1.08754	0.498
57DAP/reference	0.85941	0.022

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1013	0.65
27DAP/17DAP	1.04575	0.817
39DAP/27DAP	1.14928	0.27
41DAP/39DAP	0.95325	0.861
42DAP/41DAP	1.03351	1
43DAP/42DAP	0.97321	0.831
47DAP/43DAP	1.04156	0.822
52DAP/47DAP	0.94479	0.753
57DAP/52DAP	1.05107	0.703
57DAP/7DAP	1.33172	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86293	0.104
17DAP/reference	0.92476	0.019
27DAP/reference	0.91761	0.01
39DAP/reference	0.90228	0.021
41DAP/reference	0.90998	0.024
42DAP/reference	0.87941	0.033
43DAP/reference	0.8604	0.038
47DAP/reference	0.90591	0.128
52DAP/reference	0.81048	0.012
57DAP/reference	0.8221	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11096	0.1
17DAP/reference	1.18611	0.009
27DAP/reference	0.96272	0.467
39DAP/reference	1.07168	0.355
41DAP/reference	0.98811	0.545
42DAP/reference	0.90817	0.098
43DAP/reference	1.1638	0.037
47DAP/reference	0.96564	0.4
52DAP/reference	1.21565	0.009
57DAP/reference	1.39734	0.015

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8304	0.044
17DAP/reference	0.93964	0.374
27DAP/reference	0.89466	0.039
39DAP/reference	0.90904	0.019
41DAP/reference	0.92662	0.148
42DAP/reference	0.83794	0.036
43DAP/reference	0.83394	0.143
47DAP/reference	1.01934	1
52DAP/reference	0.76389	0.216
57DAP/reference	0.57329	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.95541	1
26DAP/20DAP	0.92057	0.512
34DAP/26DAP	1.06978	1
51DAP/34DAP	1.35686	0.057
52DAP/51DAP	0.95	1
53DAP/52DAP	1.25377	0.144
55DAP/53DAP	0.97493	0.807
57DAP/55DAP	0.86098	0.256
62DAP/57DAP	0.92426	0.681
68DAP/62DAP	0.88313	0.641
68DAP/14DAP	0.96744	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9929	0.737

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.22794	0.063
Mature Green Tomato/Ripe Tomato	0.6473	0.025
Immature Eggplant/Mature Eggplant	4.79388	0.054
Ripe Pepper/Ripe Tomato	0.97581	1
Mature Eggplant/Ripe Tomato	0.68249	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.43536	0.304
1-1-2/M82	1.08351	0.977
12-2/M82	1.05965	N/A
12-4/M82	0.74423	1
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	0.93296	N/A
3-2/M82	1.05354	1
4-1-1/M82	1.29711	N/A
4-1/M82	0.67556	N/A
4-3-2/M82	1.00962	N/A
4-3/M82	0.60958	0.611
5-3/M82	1.04294	1
6-2/M82	1.02346	1
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	0.74089	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.14631	0.277
IL2-6/WTpooled	0.85732	0.473
IL7-5/WTpooled	1.04123	1
IL7-3/WTpooled	1.06466	1
IL12-4/WTpooled	0.90544	0.539
IL1-4/WTpooled	0.94666	0.834
WT/WTpooled	1.12294	0.874

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	2.17201	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97238	1
DC3000/delta hrp 6h	1.08052	1
DC3000/delta hrp 12h	1.07777	1
DC3000/delta hrp 24h	1.23931	0.192

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.19776	0.408
DC3000 delta B/DC3000 delta AB	1.0577	0.535

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86494	1
Exp 36h	1.47678	0.693
Exp 60h	1.00233	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.04913	1
Var 0h	1.14813	0.98
Var 12h I row2-row1	1.16056	0.406
Var 12h NI row2-row1	0.99711	1
Var 36h I row2-row1	0.83053	0.575
Var 36h NI row2-row1	0.86107	0.584
Var 60h I row2-row1	1.1428	1
Var 60h NI row2-row1	1.29999	0.904
Time course 0hI-0hNI	1.12395	0.603
Time course 12hI-12hNI	0.99409	0.994
Time course 36hI-36hNI	1.07253	0.316
Time course 60hI-60hNI	1.49024	0.009

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)	1.00792	1
transgenic ySAMdc/azygous control (breaker)	1.63784	0.172
transgenic ySAMdc/azygous control (red)	0.9711	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9804	0.286

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.94608	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99298	1
Manapal/WT (break)	N/A	N/A
Manapal/WT (red)	0.60783	0.181