Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.3.2.5

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.56375	0.092
27DAP/17DAP	2.12878	0.203
39DAP/27DAP	1.04668	0.876
41DAP/39DAP	0.72401	0.136
42DAP/41DAP	1.20678	0.916
43DAP/42DAP	0.97944	0.925
47DAP/43DAP	0.77306	0.407
52DAP/47DAP	1.30299	0.641
57DAP/52DAP	0.81024	0.684

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99605	0.707
17DAP/reference	0.93694	0.26
27DAP/reference	1.14255	0.211
39DAP/reference	0.87439	0.184
41DAP/reference	0.82355	0.049
42DAP/reference	1.12674	0.219
43DAP/reference	0.99845	0.882
47DAP/reference	1.06925	0.963
52DAP/reference	1.16482	0.102
57DAP/reference	1.34329	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.6727	0.923
27DAP/17DAP	0.64006	0.179
39DAP/27DAP	0.84389	0.437
41DAP/39DAP	2.16525	0.07
42DAP/41DAP	0.61595	0.023
43DAP/42DAP	1.2175	0.273
47DAP/43DAP	1.23449	0.213
52DAP/47DAP	1.51106	0.123
57DAP/52DAP	1.70514	0.2
57DAP/7DAP	1.35046	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.44093	0.043
17DAP/reference	1.47459	0.01
27DAP/reference	1.11368	0.551
39DAP/reference	1.72701	0.006
41DAP/reference	1.18689	0.109
42DAP/reference	1.73213	0.018
43DAP/reference	1.83265	0.011
47DAP/reference	1.45233	0.038
52DAP/reference	1.82426	0.008
57DAP/reference	1.89537	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95898	0.592
17DAP/reference	0.93005	0.239
27DAP/reference	0.90359	0.249
39DAP/reference	1.1084	0.463
41DAP/reference	1.48734	0.007
42DAP/reference	1.16025	0.157
43DAP/reference	1.15042	0.489
47DAP/reference	1.49975	0.016
52DAP/reference	0.86833	0.047
57DAP/reference	1.04741	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19465	0.176
17DAP/reference	0.93553	0.488
27DAP/reference	1.08102	0.207
39DAP/reference	1.08955	0.196
41DAP/reference	1.08141	0.818
42DAP/reference	1.10717	0.612
43DAP/reference	1.47954	0.105
47DAP/reference	0.88077	0.215
52DAP/reference	1.22259	0.549
57DAP/reference	1.51909	0.015

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08344	0.966
26DAP/20DAP	1.0096	1
34DAP/26DAP	0.96228	0.92
51DAP/34DAP	0.99011	0.747
52DAP/51DAP	1.24204	0.176
53DAP/52DAP	1.30749	0.261
55DAP/53DAP	1.31029	0.306
57DAP/55DAP	1.01384	0.855
62DAP/57DAP	0.80629
68DAP/62DAP	1.79495	0.088
68DAP/14DAP	1.45827	0.055

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.72701	0.026

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.15732	1
Mature Green Tomato/Ripe Tomato	0.72861	0.317
Immature Eggplant/Mature Eggplant	1.30311	0.13
Ripe Pepper/Ripe Tomato	0.85554	1
Mature Eggplant/Ripe Tomato	0.89541	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.83166
12-2/M82	N/A	N/A
12-4/M82	0.771	0.33
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	0.60498	0.49
6-2/M82	2.15189
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.02166
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.63445	0.243
IL2-6/WTpooled	1.17765	0.46
IL7-5/WTpooled	0.80704	1
IL7-3/WTpooled	0.74931	0.418
IL12-4/WTpooled	0.94137	0.71
IL1-4/WTpooled	0.85803	0.699
WT/WTpooled	1.02333	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	2.05856	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04956	0.894
DC3000/delta hrp 6h	1.33828	1
DC3000/delta hrp 12h	0.90488	1
DC3000/delta hrp 24h	1.45052	0.058

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.62536	0.042
DC3000 delta B/DC3000 delta AB	1.70637	0.095

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01522	1
Exp 36h	1.87817	0.489
Exp 60h	1.56241	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97432	1
Var 0h	1.27194	0.263
Var 12h I row2-row1	1.32674	0.506
Var 12h NI row2-row1	1.04266	1
Var 36h I row2-row1	1.22049	0.742
Var 36h NI row2-row1	0.89199	0.645
Var 60h I row2-row1	1.29193	0.543
Var 60h NI row2-row1	0.9885	1
Time course 0hI-0hNI	0.88543	0.138
Time course 12hI-12hNI	1.30385	0.017
Time course 36hI-36hNI	2.88474	0.005
Time course 60hI-60hNI	3.80365	0.008

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)	0.85739	0.314
transgenic ySAMdc/azygous control (breaker)	1.05925	1
transgenic ySAMdc/azygous control (red)	1.22781	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04641	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.78129	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.03604	1
Manapal/WT (break)	1.50589	0.13
Manapal/WT (red)	0.87397	0.181