Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.17.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.80589	0.297
27DAP/17DAP	0.84414	0.637
39DAP/27DAP	1.04887	1
41DAP/39DAP	0.73573	0.394
42DAP/41DAP	1.04505	0.986
43DAP/42DAP	1.46689	0.271
47DAP/43DAP	1.28148	0.469
52DAP/47DAP	1.15226	0.828
57DAP/52DAP	1.08072	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95421	0.422
17DAP/reference	1.24309	0.342
27DAP/reference	0.85508	0.059
39DAP/reference	1.04308	0.445
41DAP/reference	1.022	0.808
42DAP/reference	0.91245	0.059
43DAP/reference	1.0717	0.73
47DAP/reference	1.20419	0.03
52DAP/reference	0.98333	0.618
57DAP/reference	0.90794	0.165

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.1435	0.785
27DAP/17DAP	1.17312	0.798
39DAP/27DAP	1.07051	0.603
41DAP/39DAP	1.07196	0.895
42DAP/41DAP	0.8524	0.318
43DAP/42DAP	1.05741	0.664
47DAP/43DAP	1.16556	0.325
52DAP/47DAP	0.99498	0.962
57DAP/52DAP	1.05318	0.858
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01692	0.758
17DAP/reference	1.23767	0.162
27DAP/reference	1.0645	0.453
39DAP/reference	1.43118	0.006
41DAP/reference	0.9191	0.235
42DAP/reference	1.21543	0.1
43DAP/reference	1.1564	0.637
47DAP/reference	0.93473	0.383
52DAP/reference	1.00368	0.74
57DAP/reference	1.09204	0.356

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02681	0.943
17DAP/reference	0.86608	0.033
27DAP/reference	0.95169	0.393
39DAP/reference	0.86254	0.102
41DAP/reference	0.78063	0.068
42DAP/reference	1.05124	1
43DAP/reference	1.19731	0.396
47DAP/reference	0.90476	0.126
52DAP/reference	1.00331	0.761
57DAP/reference	1.02072	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01273	0.75
17DAP/reference	1.03325	0.898
27DAP/reference	1.06535	0.805
39DAP/reference	1.08235	0.353
41DAP/reference	1.02972	0.57
42DAP/reference	0.88001	0.22
43DAP/reference	0.80192	0.081
47DAP/reference	1.25282	0.027
52DAP/reference	1.1219	0.941
57DAP/reference	1.06427	0.682

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12731	0.362
26DAP/20DAP	1.32887	0.567
34DAP/26DAP	1.27241	0.819
51DAP/34DAP	1.40567	0.775
52DAP/51DAP	0.87163	1
53DAP/52DAP	0.9498	0.817
55DAP/53DAP	0.99148	0.876
57DAP/55DAP	0.96903	0.863
62DAP/57DAP	1.09176	0.902
68DAP/62DAP	1.14942	0.821
68DAP/14DAP	1.11539	0.915

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01962	0.7

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.43707
Mature Eggplant/Ripe Tomato	0.72274

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	4.86461
12-4/M82	0.92309
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	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.19227	1
6-2/M82	N/A	N/A
6-3/M82	1.07026
7-1/M82	N/A	N/A
7-2/M82	N/A	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	0.99555	1
IL2-6/WTpooled	1.15	0.584
IL7-5/WTpooled	0.89413	1
IL7-3/WTpooled	0.97507	1
IL12-4/WTpooled	1.04696	0.532
IL1-4/WTpooled	1.10305	1
WT/WTpooled	0.9441	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	0.89401

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.992	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.09146	1
DC3000/delta hrp 24h	1.00726	1

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	0.97346
Var 0h	0.61978	0.933
Var 12h I row2-row1	1.21299	0.235
Var 12h NI row2-row1	1.50974	1
Var 36h I row2-row1	3.15712	1
Var 36h NI row2-row1	0.47261	1
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.98453	1
Time course 0hI-0hNI	1.1329	0.719
Time course 12hI-12hNI	0.99833	1
Time course 36hI-36hNI	5.95499	0.513
Time course 60hI-60hNI	0.84103	0.161

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)	1.18835	0.256
transgenic ySAMdc/azygous control (breaker)	1.11613	1
transgenic ySAMdc/azygous control (red)	0.92296	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.43626	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.98263	1
Manapal/WT (red)	0.76889	0.424