Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.10.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.64584	0.162
27DAP/17DAP	0.8705	0.665
39DAP/27DAP	1.84193	0.176
41DAP/39DAP	1.12908	0.722
42DAP/41DAP	1.03578	0.978
43DAP/42DAP	0.92138	0.801
47DAP/43DAP	1.61075	0.282
52DAP/47DAP	0.88947	0.646
57DAP/52DAP	1.10876	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02923	1
17DAP/reference	0.77496	0.074
27DAP/reference	1.01766	0.867
39DAP/reference	0.87305	0.254
41DAP/reference	0.76934	0.065
42DAP/reference	0.9376	0.182
43DAP/reference	1.22618	0.014
47DAP/reference	1.0022	0.535
52DAP/reference	1.11771	0.205
57DAP/reference	1.45496	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.60267	0.045
27DAP/17DAP	0.92421	0.241
39DAP/27DAP	0.9049	0.54
41DAP/39DAP	0.94999	0.875
42DAP/41DAP	0.98504	0.791
43DAP/42DAP	0.8124	0.049
47DAP/43DAP	0.84325	0.347
52DAP/47DAP	2.13175	0.051
57DAP/52DAP	1.83359	0.089
57DAP/7DAP	1.71027	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49042	0.025
17DAP/reference	1.92765	0.022
27DAP/reference	1.51396	0.008
39DAP/reference	2.3543	0.005
41DAP/reference	2.05096	0.014
42DAP/reference	2.12022	0.007
43DAP/reference	2.64179	0.009
47DAP/reference	1.41654	0.298
52DAP/reference	1.67685	0.066
57DAP/reference	1.37601	0.033

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75994	0.064
17DAP/reference	0.58217	0.005
27DAP/reference	0.77039	0.049
39DAP/reference	0.79476	0.074
41DAP/reference	0.93418	0.307
42DAP/reference	0.81552	0.013
43DAP/reference	0.57	0.011
47DAP/reference	0.66337	0.009
52DAP/reference	0.68258	0.005
57DAP/reference	0.473	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.69127	0.033
17DAP/reference	1.28157	0.488
27DAP/reference	1.89369	0.02
39DAP/reference	1.51795	0.023
41DAP/reference	1.5874	0.011
42DAP/reference	1.97311	0.009
43DAP/reference	1.55882	0.021
47DAP/reference	0.87931	0.199
52DAP/reference	3.3319	0.085
57DAP/reference	1.32298	0.164

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.01271	1
26DAP/20DAP	2.66234	0.555
34DAP/26DAP	2.59274	1
51DAP/34DAP	1.66703	0.775
52DAP/51DAP	2.76404	0.035
53DAP/52DAP	0.88454	0.329
55DAP/53DAP	1.17095	0.589
57DAP/55DAP	0.36676	0.01
62DAP/57DAP	1.35635	0.158
68DAP/62DAP	4.61938	0.029
68DAP/14DAP	5.12963	0.016

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.52387	0.022

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.40528	0.04
Immature Eggplant/Mature Eggplant	3.95294	0.05
Ripe Pepper/Ripe Tomato	0.08154	0.224
Mature Eggplant/Ripe Tomato	0.19976	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.48149	0.877
1-1-2/M82	1.0336	1
12-2/M82	0.88678	0.955
12-4/M82	1.43639	1
1-3/M82	1.19187	1
2-1-1/M82	1.42661	0.236
2-1/M82	1.44084	0.32
2-6/M82	0.7425	0.501
3-2/M82	1.6635	0.463
4-1-1/M82	0.81575	1
4-1/M82	1.04697	0.853
4-3-2/M82	0.78591	0.698
4-3/M82	1.49324	1
5-3/M82	1.212	0.572
6-2/M82	1.16678	1
6-3/M82	0.85317	1
7-1/M82	1.01234	1
7-2/M82	1.03699	1
9-3-2/M82	0.83281	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08469	1
IL2-6/WTpooled	1.1958	0.788
IL7-5/WTpooled	0.97338
IL7-3/WTpooled	0.87487
IL12-4/WTpooled	0.6215	0.581
IL1-4/WTpooled	1.00216	1
WT/WTpooled	1.14482	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	0.87807	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99489	1
DC3000/delta hrp 6h	1.12124	1
DC3000/delta hrp 12h	1.068	1
DC3000/delta hrp 24h	0.9967	0.978

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.17405	0.229
DC3000 delta B/DC3000 delta AB	1.19344	0.394

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95372	1
Exp 36h	2.01219	0.349
Exp 60h	1.39823	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02722	1
Var 0h	0.92109	0.933
Var 12h I row2-row1	0.72863	0.514
Var 12h NI row2-row1	1.34228	0.34
Var 36h I row2-row1	1.05122	1
Var 36h NI row2-row1	1.20742	0.482
Var 60h I row2-row1	0.92735	0.832
Var 60h NI row2-row1	0.85537	0.977
Time course 0hI-0hNI	0.85765	0.151
Time course 12hI-12hNI	0.91749	0.606
Time course 36hI-36hNI	0.96045	0.418
Time course 60hI-60hNI	0.909	0.319

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)	0.75665	0.213
transgenic ySAMdc/azygous control (breaker)	0.85609	0.49
transgenic ySAMdc/azygous control (red)	1.17144	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.114	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.1715	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.67636	1
Manapal/WT (break)	0.79588	1
Manapal/WT (red)	1.17375	0.222