Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.1.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.29155	0.381
27DAP/17DAP	0.48239	0.035
39DAP/27DAP	0.70328	0.397
41DAP/39DAP	0.45083	0.041
42DAP/41DAP	0.70757	0.774
43DAP/42DAP	1.40475	0.671
47DAP/43DAP	0.34313	0.049
52DAP/47DAP	1.17622	0.946
57DAP/52DAP	0.93648	0.853

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65172	0.03
17DAP/reference	0.56833	0.012
27DAP/reference	0.55252	0.013
39DAP/reference	0.58018	0.018
41DAP/reference	0.38537	0.008
42DAP/reference	0.48271	0.001
43DAP/reference	0.40548	0.013
47DAP/reference	0.41852	0.001
52DAP/reference	0.31595	0.012
57DAP/reference	0.44196	0.008

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.94052	0.036
27DAP/17DAP	0.6758	0.218
39DAP/27DAP	0.31018	0.028
41DAP/39DAP	1.41093	0.091
42DAP/41DAP	0.78338	0.024
43DAP/42DAP	0.50758	0.022
47DAP/43DAP	0.8058	0.134
52DAP/47DAP	0.85072	0.466
57DAP/52DAP	0.87869	0.322
57DAP/7DAP	1.08091	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93398	0.326
17DAP/reference	0.70003	0.011
27DAP/reference	0.48174	0.01
39DAP/reference	0.40881	0.011
41DAP/reference	0.38558	0.009
42DAP/reference	0.46412	0.012
43DAP/reference	0.35182	0.011
47DAP/reference	0.33658	0.026
52DAP/reference	0.33481	0.009
57DAP/reference	0.37789	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.45008	0.005
17DAP/reference	0.46801	0.004
27DAP/reference	0.51254	0.008
39DAP/reference	0.30627	0.007
41DAP/reference	0.41122	0.007
42DAP/reference	0.59549	0.046
43DAP/reference	0.28361	0.002
47DAP/reference	0.47659	0.011
52DAP/reference	0.32832	0.003
57DAP/reference	0.25287	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.86643	0.016
17DAP/reference	1.57579	0.11
27DAP/reference	1.08216	0.552
39DAP/reference	0.87361	0.299
41DAP/reference	0.70697	0.03
42DAP/reference	0.45709	0.016
43DAP/reference	0.41409	0.014
47DAP/reference	0.39112	0.005
52DAP/reference	0.49925	0.066
57DAP/reference	0.87154	0.238

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18953	0.945
26DAP/20DAP	1.05851	1
34DAP/26DAP	0.87651	0.455
51DAP/34DAP	0.44532	0.049
52DAP/51DAP	1.10588	0.776
53DAP/52DAP	0.64711	0.049
55DAP/53DAP	0.67879	0.055
57DAP/55DAP	1.20032	0.728
62DAP/57DAP	1.4723	0.004
68DAP/62DAP	0.79716	0.464
68DAP/14DAP	0.78259	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.4329	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.45023	0.058
Mature Green Tomato/Ripe Tomato	14.9459	0.015
Immature Eggplant/Mature Eggplant	0.56422	0.062
Ripe Pepper/Ripe Tomato	17.22	0.256
Mature Eggplant/Ripe Tomato	37.3511	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.86113
12-2/M82	N/A	N/A
12-4/M82	1.04327	1
1-3/M82	1.04546
2-1-1/M82	0.70452	0.683
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	0.78545
5-3/M82	2.19098	0.496
6-2/M82	N/A	N/A
6-3/M82	1.27032
7-1/M82	1.17275
7-2/M82	1.04239	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.01464	0.493
IL2-6/WTpooled	0.75739	0.473
IL7-5/WTpooled	1.05542	1
IL7-3/WTpooled	1.06574	1
IL12-4/WTpooled	0.87937	0.71
IL1-4/WTpooled	0.77673	0.435
WT/WTpooled	0.99746	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	1.20983	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10001	1
DC3000/delta hrp 6h	1.16116	1
DC3000/delta hrp 12h	1.00207	1
DC3000/delta hrp 24h	0.91682	0.523

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.79524	0.085
DC3000 delta B/DC3000 delta AB	0.65332	0.075

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00299	1
Exp 36h	0.9041	0.699
Exp 60h	0.79622	0.251

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94867	1
Var 0h	0.97633	1
Var 12h I row2-row1	0.99796	1
Var 12h NI row2-row1	0.99484	1
Var 36h I row2-row1	0.8919	0.805
Var 36h NI row2-row1	0.94632	0.706
Var 60h I row2-row1	1.45191	0.543
Var 60h NI row2-row1	0.91428	0.483
Time course 0hI-0hNI	0.9891	0.999
Time course 12hI-12hNI	1.13186	0.19
Time course 36hI-36hNI	1.13417	0.218
Time course 60hI-60hNI	0.64078	0.081

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)	1.11395	0.798
transgenic ySAMdc/azygous control (breaker)	2.20673	0.162
transgenic ySAMdc/azygous control (red)	1.22172	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.607	0.14

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.68334	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	24.2104	0.083
Manapal/WT (break)	8.66868	0.123
Manapal/WT (red)	3.48036	0.413