Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.7.11

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.14828	0.602
27DAP/17DAP	0.65042	0.101
39DAP/27DAP	0.84759	0.522
41DAP/39DAP	0.74722	0.133
42DAP/41DAP	1.02605	1
43DAP/42DAP	1.14263	0.793
47DAP/43DAP	0.88381	0.613
52DAP/47DAP	1.05349	0.941
57DAP/52DAP	0.87156	0.836

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99593	0.743
17DAP/reference	1.00368	0.907
27DAP/reference	0.99234	0.779
39DAP/reference	0.95396	0.333
41DAP/reference	0.96568	0.434
42DAP/reference	0.93228	0.01
43DAP/reference	0.93389	0.302
47DAP/reference	0.88999	0.005
52DAP/reference	0.80502	0.027
57DAP/reference	0.94864	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.25611	0.083
27DAP/17DAP	0.94221	0.724
39DAP/27DAP	0.84166	0.089
41DAP/39DAP	1.05888	0.55
42DAP/41DAP	0.91198	0.466
43DAP/42DAP	1.10985	0.147
47DAP/43DAP	0.99166	0.971
52DAP/47DAP	0.93461	0.719
57DAP/52DAP	0.9572	0.498
57DAP/7DAP	1.06571	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05671	0.452
17DAP/reference	0.95075	0.22
27DAP/reference	0.83197	0.01
39DAP/reference	0.86301	0.011
41DAP/reference	0.80888	0.016
42DAP/reference	0.78411	0.011
43DAP/reference	0.82554	0.023
47DAP/reference	0.80639	0.038
52DAP/reference	0.82912	0.012
57DAP/reference	0.88962	0.028

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96648	0.592
17DAP/reference	0.98654	0.626
27DAP/reference	0.93342	0.173
39DAP/reference	0.84366	0.009
41DAP/reference	0.90583	0.059
42DAP/reference	0.90452	0.035
43DAP/reference	0.7474	0.005
47DAP/reference	0.91909	0.029
52DAP/reference	0.83689	0.005
57DAP/reference	0.8255	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1647	0.043
17DAP/reference	1.26678	0.07
27DAP/reference	1.08636	0.237
39DAP/reference	1.05569	0.285
41DAP/reference	1.03531	0.605
42DAP/reference	0.77199	0.014
43DAP/reference	0.91113	0.092
47DAP/reference	0.87863	0.008
52DAP/reference	0.7728	0.066
57DAP/reference	1.13948	0.233

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.93306	0.281
26DAP/20DAP	0.88374	0.512
34DAP/26DAP	1.10694	0.542
51DAP/34DAP	0.99672	0.927
52DAP/51DAP	0.93546	1
53DAP/52DAP	0.88237	0.498
55DAP/53DAP	1.15403	0.312
57DAP/55DAP	0.97418	0.888
62DAP/57DAP	1.16874	0.767
68DAP/62DAP	1.29905	0.523
68DAP/14DAP	1.38355	0.403

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.01798	0.74

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.1946	0.058
Mature Green Tomato/Ripe Tomato	4.59582	0.018
Immature Eggplant/Mature Eggplant	0.96016	0.594
Ripe Pepper/Ripe Tomato	1.09453	1
Mature Eggplant/Ripe Tomato	5.79523	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04087	0.526
1-1-2/M82	0.95328	1
12-2/M82	1.02647	1
12-4/M82	1.00559	1
1-3/M82	0.92246	0.378
2-1-1/M82	1.24023	0.764
2-1/M82	1.01471	1
2-6/M82	1.05105	0.695
3-2/M82	0.99821
4-1-1/M82	0.96966	1
4-1/M82	1.04839	1
4-3-2/M82	1.03197	1
4-3/M82	1.09259	1
5-3/M82	1.04995	1
6-2/M82	1.11416	1
6-3/M82	1.03888	1
7-1/M82	1.02596	1
7-2/M82	1.13926	1
9-3-2/M82	0.91304	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.49652	0.395
IL7-5/WTpooled	0.38721
IL7-3/WTpooled	0.71176	0.294
IL12-4/WTpooled	1.23351	0.538
IL1-4/WTpooled	0.93447	1
WT/WTpooled	1.11963	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	1.09965	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91378	0.868
DC3000/delta hrp 6h	1.1552	0.978
DC3000/delta hrp 12h	1.11192	1
DC3000/delta hrp 24h	0.91328	0.319

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.62234	0.023
DC3000 delta B/DC3000 delta AB	0.59439	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96647	1
Exp 36h	0.90079	0.699
Exp 60h	0.87712	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98243	1
Var 0h	0.83914	0.933
Var 12h I row2-row1	0.99056	1
Var 12h NI row2-row1	0.98147	0.906
Var 36h I row2-row1	0.94746	1
Var 36h NI row2-row1	1.16773	1
Var 60h I row2-row1	1.14586	0.562
Var 60h NI row2-row1	1.08782	1
Time course 0hI-0hNI	1.04055	0.852
Time course 12hI-12hNI	0.98776	0.953
Time course 36hI-36hNI	1.02353	0.799
Time course 60hI-60hNI	0.37723	0.006

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)	1.16049	0.699
transgenic ySAMdc/azygous control (breaker)	3.00082	0.172
transgenic ySAMdc/azygous control (red)	1.12501	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.84781	0.131

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.63214	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.69612	0.084
Manapal/WT (break)	3.71089	0.13
Manapal/WT (red)	6.43467	0.137