Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.1.20.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	3.08947	0.07
27DAP/17DAP	1.38138	0.653
39DAP/27DAP	1.52701	0.128
41DAP/39DAP	1.02261	1
42DAP/41DAP	1.15198	0.825
43DAP/42DAP	0.85322	0.684
47DAP/43DAP	1.27187	0.633
52DAP/47DAP	0.73795	0.325
57DAP/52DAP	1.42978	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80802	0.036
17DAP/reference	1.10687	0.399
27DAP/reference	0.97501	0.514
39DAP/reference	1.0987	0.301
41DAP/reference	0.97408	0.667
42DAP/reference	1.05255	0.398
43DAP/reference	0.93083	0.273
47DAP/reference	0.98244	0.473
52DAP/reference	1.06665	0.498
57DAP/reference	0.9888	0.639

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26644	0.699
27DAP/17DAP	0.96576	0.887
39DAP/27DAP	1.07254	0.672
41DAP/39DAP	0.7054	0.333
42DAP/41DAP	0.90958	0.607
43DAP/42DAP	1.22588	0.324
47DAP/43DAP	0.96049	0.833
52DAP/47DAP	1.12758	0.645
57DAP/52DAP	0.92999	0.665
57DAP/7DAP	1.5301	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.68358	0.04
17DAP/reference	2.74448	0.006
27DAP/reference	2.81281	0.006
39DAP/reference	3.26943	0.005
41DAP/reference	2.29445	0.062
42DAP/reference	3.72541
43DAP/reference	4.91477	0.006
47DAP/reference	2.41762	0.104
52DAP/reference	4.18814	0.007
57DAP/reference	3.30725	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80324	0.046
17DAP/reference	0.9106	0.124
27DAP/reference	0.98586	0.598
39DAP/reference	0.94016	0.416
41DAP/reference	0.90837	0.194
42DAP/reference	1.3345	0.129
43DAP/reference	1.07282	0.777
47DAP/reference	1.06965	0.218
52DAP/reference	0.88047	0.101
57DAP/reference	0.97624	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.8268	0.031
17DAP/reference	1.30844	0.398
27DAP/reference	2.37089	0.017
39DAP/reference	2.21101	0.013
41DAP/reference	2.22108	0.007
42DAP/reference	2.70592	0.024
43DAP/reference	2.08522	0.039
47DAP/reference	0.95798	0.421
52DAP/reference	3.2412	0.048
57DAP/reference	1.76095	0.501

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.4839	0.966
26DAP/20DAP	0.68347	0.512
34DAP/26DAP	0.56717	0.093
51DAP/34DAP	1.04776
52DAP/51DAP	0.58664	1
53DAP/52DAP	1.09025	0.998
55DAP/53DAP	1.15427	0.712
57DAP/55DAP	0.9354	0.633
62DAP/57DAP	0.94771	0.994
68DAP/62DAP	1.33089	0.872
68DAP/14DAP	0.729	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.66328	0.378

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.65692	0.048
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	0.34059

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96714	0.961
1-1-2/M82	1.05037
12-2/M82	N/A	N/A
12-4/M82	1.18915	0.611
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	0.95018	1
3-2/M82	0.89582	0.752
4-1-1/M82	N/A	N/A
4-1/M82	1.70505
4-3-2/M82	1.80774
4-3/M82	N/A	N/A
5-3/M82	0.92763	1
6-2/M82	N/A	N/A
6-3/M82	1.04797	1
7-1/M82	1.32052
7-2/M82	0.93365
9-3-2/M82	1.57603	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.81214
WT/WTpooled	N/A	N/A

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	1.24451	0.309

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00952	1
DC3000/delta hrp 6h	2.76907
DC3000/delta hrp 12h	1.08851	1
DC3000/delta hrp 24h	0.99142	0.988

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	2.53069
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	1.86808	1
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	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.47206	0.326
transgenic ySAMdc/azygous control (breaker)	0.64708	0.137
transgenic ySAMdc/azygous control (red)	0.98454	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.93527	0.191

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.72259	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.92321	1
Manapal/WT (break)	0.61799	0.333
Manapal/WT (red)	0.58441	0.229