Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.20.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02697	0.951
27DAP/17DAP	0.82291	0.604
39DAP/27DAP	0.91276	0.663
41DAP/39DAP	1.61401	0.288
42DAP/41DAP	2.04548	0.899
43DAP/42DAP	1.06222	0.945
47DAP/43DAP	0.91772	0.68
52DAP/47DAP	1.20479	0.891
57DAP/52DAP	2.30863	0.878

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89954	0.149
17DAP/reference	0.77232	0.017
27DAP/reference	0.9356	0.417
39DAP/reference	1.0423	0.262
41DAP/reference	0.85438	0.039
42DAP/reference	0.90538	0.014
43DAP/reference	0.95264	0.48
47DAP/reference	1.02433	0.862
52DAP/reference	1.18962	0.045
57DAP/reference	1.17478	0.041

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.34482	0.208
27DAP/17DAP	1.11259	0.798
39DAP/27DAP	1.25012	0.378
41DAP/39DAP	1.06615	0.817
42DAP/41DAP	1.02638	0.935
43DAP/42DAP	0.95906	0.665
47DAP/43DAP	1.17273	0.325
52DAP/47DAP	1.25112	0.296
57DAP/52DAP	0.97885	0.776
57DAP/7DAP	1.58572	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89185	0.078
17DAP/reference	1.02938	0.971
27DAP/reference	1.13925	0.131
39DAP/reference	1.00388	0.745
41DAP/reference	1.16699	0.015
42DAP/reference	1.38163	0.174
43DAP/reference	1.08449	0.457
47DAP/reference	1.03516	0.868
52DAP/reference	1.01977	1
57DAP/reference	1.0691	0.571

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.20975	0.384
17DAP/reference	1.03485	0.739
27DAP/reference	1.06024	0.562
39DAP/reference	0.97499	0.469
41DAP/reference	1.01087	0.749
42DAP/reference	1.18401	0.013
43DAP/reference	1.42049	0.082
47DAP/reference	1.08022	0.264
52DAP/reference	1.29862	0.02
57DAP/reference	1.10896	0.581

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90148	0.059
17DAP/reference	1.02111	1
27DAP/reference	1.16441	0.934
39DAP/reference	0.94342	0.299
41DAP/reference	1.02712	0.826
42DAP/reference	1.13453	0.287
43DAP/reference	0.9214	0.165
47DAP/reference	1.06994	0.294
52DAP/reference	0.89469	0.334
57DAP/reference	1.2981	0.132

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.04261	1
26DAP/20DAP	1.0239	1
34DAP/26DAP	0.99486	1
51DAP/34DAP	1.21384	0.706
52DAP/51DAP	0.78247	1
53DAP/52DAP	0.96844	0.862
55DAP/53DAP	1.20317	0.193
57DAP/55DAP	0.91744	0.647
62DAP/57DAP	1.31012	0.767
68DAP/62DAP	1.35747	0.166
68DAP/14DAP	1.94589	0.046

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.58537	0.024

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.05582	0.485
Ripe Pepper/Ripe Tomato	0.08543	0.224
Mature Eggplant/Ripe Tomato	0.81231	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.05477	1
1-1-2/M82	0.89169
12-2/M82	1.16643
12-4/M82	0.90107	0.358
1-3/M82	1.27127	1
2-1-1/M82	0.83289
2-1/M82	1.33883	0.335
2-6/M82	0.88778	1
3-2/M82	N/A	N/A
4-1-1/M82	0.99057	1
4-1/M82	1.63637
4-3-2/M82	N/A	N/A
4-3/M82	1.08709	1
5-3/M82	0.9519	1
6-2/M82	0.72764	0.473
6-3/M82	0.77063	1
7-1/M82	N/A	N/A
7-2/M82	0.97407	0.599
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.6057	0.243
IL2-6/WTpooled	1.37363	0.419
IL7-5/WTpooled	1.11399	1
IL7-3/WTpooled	0.59552	0.31
IL12-4/WTpooled	0.8322	0.581
IL1-4/WTpooled	0.69827	0.444
WT/WTpooled	0.92645	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	1.04529	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97649	1
DC3000/delta hrp 6h	0.94229	0.95
DC3000/delta hrp 12h	0.94408	1
DC3000/delta hrp 24h	0.97562	0.91

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.73481	0.042
DC3000 delta B/DC3000 delta AB	1.21126	0.292

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.15883	0.196
Exp 36h	1.12816	0.489
Exp 60h	1.44578	0.226

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

hybridization	ratio	FDR (corrected p value)
self-self	0.97754	1
Var 0h	N/A	N/A
Var 12h I row2-row1	0.938	0.77
Var 12h NI row2-row1	1.14493	1
Var 36h I row2-row1	0.97739	1
Var 36h NI row2-row1	1.06176	1
Var 60h I row2-row1	0.91728	0.952
Var 60h NI row2-row1	0.84738	0.458
Time course 0hI-0hNI	0.98007	0.927
Time course 12hI-12hNI	0.95421	0.501
Time course 36hI-36hNI	1.35607	0.006
Time course 60hI-60hNI	1.41388	0.011

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)	1.00649	0.863
transgenic ySAMdc/azygous control (breaker)	0.85463	0.173
transgenic ySAMdc/azygous control (red)	0.90289	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08277	0.096

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74216	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.77669	0.172
Manapal/WT (break)	0.82455	0.333
Manapal/WT (red)	0.54872	0.181