Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.4.10.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.24655	0.014
27DAP/17DAP	0.38623	0.027
39DAP/27DAP	0.86318	0.583
41DAP/39DAP	0.86609	0.619
42DAP/41DAP	0.92396	1
43DAP/42DAP	0.88715	0.846
47DAP/43DAP	0.89149	0.667
52DAP/47DAP	1.00433	0.933
57DAP/52DAP	1.11362	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40729	0.421
17DAP/reference	0.1368	0.007
27DAP/reference	0.13193	0.009
39DAP/reference	0.20528	0.009
41DAP/reference	0.10187	0.008
42DAP/reference	0.11055	0.001
43DAP/reference	0.10678	0.012
47DAP/reference	0.10582	0.001
52DAP/reference	0.12122	0.012
57DAP/reference	0.14875	0.006

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.14694	0.016
27DAP/17DAP	0.84316	0.648
39DAP/27DAP	1.0299	0.845
41DAP/39DAP	0.9463	0.91
42DAP/41DAP	1.03692	0.894
43DAP/42DAP	0.98032	0.854
47DAP/43DAP	1.0154	1
52DAP/47DAP	0.84833	0.6
57DAP/52DAP	0.9613	0.721
57DAP/7DAP	0.2976	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.38766	0.047
17DAP/reference	0.27418	0.011
27DAP/reference	0.27038	0.01
39DAP/reference	0.22783	0.011
41DAP/reference	0.51009	0.026
42DAP/reference	0.26711	0.01
43DAP/reference	0.21841	0.009
47DAP/reference	0.15024	0.03
52DAP/reference	0.18702	0.009
57DAP/reference	0.16989	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04915	0.907
17DAP/reference	0.15974	0.003
27DAP/reference	0.12931	0.005
39DAP/reference	0.10372	0.008
41DAP/reference	0.27923	0.007
42DAP/reference	0.11737	0.01
43DAP/reference	0.10162	0.002
47DAP/reference	0.17025	0.007
52DAP/reference	0.09811	0.003
57DAP/reference	0.17849	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.3617	0.804
17DAP/reference	0.51282	0.097
27DAP/reference	0.23639	0.031
39DAP/reference	0.26339	0.012
41DAP/reference	0.22137	0.018
42DAP/reference	0.24039	0.016
43DAP/reference	0.23431	0.021
47DAP/reference	0.04645	0.004
52DAP/reference	0.1908	0.06
57DAP/reference	0.1087	0.016

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.24469	0.966
26DAP/20DAP	1.00884	1
34DAP/26DAP	1.05266	1
51DAP/34DAP	0.83077	0.259
52DAP/51DAP	1.04507	0.954
53DAP/52DAP	1.04864	0.91
55DAP/53DAP	1.00981	0.917
57DAP/55DAP	1.01764	0.955
62DAP/57DAP	1.31051	0.133
68DAP/62DAP	0.84342	0.144
68DAP/14DAP	1.24023	0.453

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90601	0.304

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	8.37234	0.015
Immature Eggplant/Mature Eggplant	15.1181	1
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	N/A	N/A
12-4/M82	N/A	N/A
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	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
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	0.75191
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78778	1
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.15754	1
WT/WTpooled	1.20918	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	0.71298	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99688	1
DC3000/delta hrp 6h	1.25368	0.672
DC3000/delta hrp 12h	0.14369	0.386
DC3000/delta hrp 24h	13.0627	0.043

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.86552	0.042
DC3000 delta B/DC3000 delta AB	1.40118	0.106

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.5526	0.661
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	0.9841	1
Var 0h	1.01614	1
Var 12h I row2-row1	0.95415	0.418
Var 12h NI row2-row1	0.96504	0.82
Var 36h I row2-row1	1.02532	1
Var 36h NI row2-row1	1.267	1
Var 60h I row2-row1	0.94449	0.582
Var 60h NI row2-row1	0.81017	1
Time course 0hI-0hNI	0.86281	0.079
Time course 12hI-12hNI	0.93062	0.231
Time course 36hI-36hNI	0.8096	0.026
Time course 60hI-60hNI	0.2325	0.005

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)	1.70138	0.921
transgenic ySAMdc/azygous control (breaker)	1.59667	0.248
transgenic ySAMdc/azygous control (red)	1.22609	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.90413	0.046

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.21488	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.87099	0.105
Manapal/WT (break)	1.05802	1
Manapal/WT (red)	1.08798	1