Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.16.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.26153	0.336
27DAP/17DAP	1.07866	0.922
39DAP/27DAP	1.01359	0.84
41DAP/39DAP	1.17712	0.701
42DAP/41DAP	0.99548	1
43DAP/42DAP	1.03565	1
47DAP/43DAP	1.10579	0.856
52DAP/47DAP	0.99915	0.964
57DAP/52DAP	1.00406	0.995

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.67434	0.044
17DAP/reference	0.63456	0.024
27DAP/reference	0.60451	0.02
39DAP/reference	0.59358	0.027
41DAP/reference	0.54711	0.031
42DAP/reference	0.79901	0.028
43DAP/reference	0.7755	0.118
47DAP/reference	0.91558	0.161
52DAP/reference	0.70577	0.067
57DAP/reference	0.92347	0.042

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0098	0.99
27DAP/17DAP	1.15623
39DAP/27DAP	0.95517	0.682
41DAP/39DAP	0.98871	1
42DAP/41DAP	1.01645	0.976
43DAP/42DAP	0.93167	0.641
47DAP/43DAP	0.98119	0.861
52DAP/47DAP	0.98474	0.93
57DAP/52DAP	0.96266	0.581
57DAP/7DAP	0.91332	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8138	0.122
17DAP/reference	0.83523	0.064
27DAP/reference	0.84726	0.066
39DAP/reference	0.80454	0.011
41DAP/reference	0.86551	0.146
42DAP/reference	0.785	0.013
43DAP/reference	0.66518	0.011
47DAP/reference	0.93575	0.504
52DAP/reference	0.78301	0.038
57DAP/reference	0.70096	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69414	0.062
17DAP/reference	0.78033	0.046
27DAP/reference	0.86738	0.212
39DAP/reference	0.69243	0.06
41DAP/reference	0.98626	0.505
42DAP/reference	0.98104	0.534
43DAP/reference	0.69645	0.004
47DAP/reference	0.7536	0.021
52DAP/reference	0.49453	0.007
57DAP/reference	0.51639	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91323	0.183
17DAP/reference	0.91507	0.268
27DAP/reference	0.80852	0.119
39DAP/reference	0.81639	0.011
41DAP/reference	0.90102	0.167
42DAP/reference	0.83012	0.059
43DAP/reference	0.77966	0.03
47DAP/reference	1.02461	1
52DAP/reference	0.86768	0.342
57DAP/reference	1.37207	0.085

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99397	1
26DAP/20DAP	0.97595	1
34DAP/26DAP	1.05292	0.819
51DAP/34DAP	1.05966	0.473
52DAP/51DAP	1.04217	0.704
53DAP/52DAP	1.02166	0.868
55DAP/53DAP	1.12119	0.656
57DAP/55DAP	0.88395	0.516
62DAP/57DAP	1.16835	0.622
68DAP/62DAP	1.25211	0.316
68DAP/14DAP	1.2762	0.146

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89018	0.122

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.72861	0.202
Mature Green Tomato/Ripe Tomato	0.96082	0.569
Immature Eggplant/Mature Eggplant	0.85221	0.254
Ripe Pepper/Ripe Tomato	2.14497	0.256
Mature Eggplant/Ripe Tomato	0.9049	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.96493
12-2/M82	0.82839
12-4/M82	1.01333	1
1-3/M82	1.02746
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	0.91846	1
4-1-1/M82	1.02544	1
4-1/M82	0.93799	0.737
4-3-2/M82	0.92532	1
4-3/M82	0.74102
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.78665
7-2/M82	N/A	N/A
9-3-2/M82	0.8309	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.86723	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.02282	1
IL12-4/WTpooled	1.13115	0.516
IL1-4/WTpooled	0.81477
WT/WTpooled	0.8745	0.764

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	1.00626	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91277	1
DC3000/delta hrp 6h	1.04855	1
DC3000/delta hrp 12h	1.06137	1
DC3000/delta hrp 24h	1.1003	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.9562	0.841
DC3000 delta B/DC3000 delta AB	1.09753	0.363

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09948	0.254
Exp 36h	1.10257	1
Exp 60h	1.23755	0.221

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

hybridization	ratio	FDR (corrected p value)
self-self	1.00476	1
Var 0h	0.63294	0.594
Var 12h I row2-row1	1.01764	0.654
Var 12h NI row2-row1	0.94398	0.713
Var 36h I row2-row1	1.00857	1
Var 36h NI row2-row1	0.88998	0.645
Var 60h I row2-row1	0.99197	0.832
Var 60h NI row2-row1	1.03612	1
Time course 0hI-0hNI	1.0422	0.833
Time course 12hI-12hNI	1.02268	0.724
Time course 36hI-36hNI	1.1041	0.021
Time course 60hI-60hNI	1.25195	0.025

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)	1.24692	0.272
transgenic ySAMdc/azygous control (breaker)	1.16997	1
transgenic ySAMdc/azygous control (red)	0.94479	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.49389	0.081

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.95744	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.13662	0.14
Manapal/WT (break)	1.22184	1
Manapal/WT (red)	N/A	N/A