Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.4.13.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98303	0.83
27DAP/17DAP	0.99534	0.963
39DAP/27DAP	0.8696	0.512
41DAP/39DAP	1.41236	0.323
42DAP/41DAP	0.97282	1
43DAP/42DAP	0.89318	0.783
47DAP/43DAP	0.9084	0.687
52DAP/47DAP	1.26942	0.57
57DAP/52DAP	1.03362	0.996

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03982	0.5
17DAP/reference	0.9725	0.393
27DAP/reference	1.00295	1
39DAP/reference	1.01007	0.76
41DAP/reference	1.01942	0.48
42DAP/reference	1.03772	0.231
43DAP/reference	0.99489	0.861
47DAP/reference	0.9743	0.322
52DAP/reference	1.1189	0.302
57DAP/reference	1.09674	0.025

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95632	0.578
27DAP/17DAP	0.9706	0.614
39DAP/27DAP	1.01388	0.779
41DAP/39DAP	1.05594	0.455
42DAP/41DAP	0.96863	0.693
43DAP/42DAP	0.99612	0.991
47DAP/43DAP	1.01719	0.906
52DAP/47DAP	0.94956	0.777
57DAP/52DAP	1.0212	0.891
57DAP/7DAP	0.97636	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02459
17DAP/reference	0.99222	0.389
27DAP/reference	1.06843	0.453
39DAP/reference	0.98827	0.552
41DAP/reference	1.01754	0.745
42DAP/reference	1.07823	0.024
43DAP/reference	1.01552	0.603
47DAP/reference	0.95348	0.293
52DAP/reference	1.0026	1
57DAP/reference	1.07676	0.41

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03558	0.35
17DAP/reference	1.09027	0.294
27DAP/reference	1.02541	0.781
39DAP/reference	1.0214	0.824
41DAP/reference	1.00143	0.718
42DAP/reference	1.03311	0.744
43DAP/reference	1.04264	0.647
47DAP/reference	1.01536	0.658
52DAP/reference	0.97541	0.407
57DAP/reference	1.00943	0.807

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00343	1
17DAP/reference	1.01434	0.887
27DAP/reference	1.00985	0.903
39DAP/reference	1.05531	0.342
41DAP/reference	1.02551	0.674
42DAP/reference	1.05652	0.481
43DAP/reference	1.03655	0.58
47DAP/reference	1.01961	0.792
52DAP/reference	1.00433	1
57DAP/reference	1.00854	1

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96461	1
26DAP/20DAP	0.98914	1
34DAP/26DAP	0.97607	0.94
51DAP/34DAP	0.98042	0.779
52DAP/51DAP	1.00183	1
53DAP/52DAP	0.93155	0.75
55DAP/53DAP	0.98559	0.864
57DAP/55DAP	0.86922	0.452
62DAP/57DAP	1.00305	1
68DAP/62DAP	1.05427	0.827
68DAP/14DAP	1.10488	0.265

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02789	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.23305	1
Mature Green Tomato/Ripe Tomato	0.84056	0.107
Immature Eggplant/Mature Eggplant	1.01099	1
Ripe Pepper/Ripe Tomato	0.96666	1
Mature Eggplant/Ripe Tomato	0.78852	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.8974	0.841
1-1-2/M82	1.02177	1
12-2/M82	0.94545	0.955
12-4/M82	0.94558	1
1-3/M82	1.00457	1
2-1-1/M82	0.96814	1
2-1/M82	1.52108	1
2-6/M82	0.90153	1
3-2/M82	0.90313	0.752
4-1-1/M82	1.1038	1
4-1/M82	0.99358	1
4-3-2/M82	0.91664	1
4-3/M82	0.91538	0.72
5-3/M82	0.92734	1
6-2/M82	1.09462	1
6-3/M82	0.98616	1
7-1/M82	1.07677	0.598
7-2/M82	0.89546	0.796
9-3-2/M82	0.78915	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91825	1
IL2-6/WTpooled	0.83704	1
IL7-5/WTpooled	0.6779
IL7-3/WTpooled	0.99057	1
IL12-4/WTpooled	1.12842	0.695
IL1-4/WTpooled	0.93736	0.834
WT/WTpooled	1.01804	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	1.28507	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.00076	1
DC3000/delta hrp 6h	1.17639	1
DC3000/delta hrp 12h	1.01884	1
DC3000/delta hrp 24h	1.04959	0.422

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.16485	0.11
DC3000 delta B/DC3000 delta AB	1.11024	0.324

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88088	1
Exp 36h	0.77709	0.406
Exp 60h	1.10365	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95853	1
Var 0h	0.88459	0.936
Var 12h I row2-row1	1.17982	0.196
Var 12h NI row2-row1	1.00975	1
Var 36h I row2-row1	1.0786	1
Var 36h NI row2-row1	0.88794	0.645
Var 60h I row2-row1	1.08344	1
Var 60h NI row2-row1	1.07398	1
Time course 0hI-0hNI	1.09126	0.833
Time course 12hI-12hNI	1.08529	0.709
Time course 36hI-36hNI	1.0745	0.218
Time course 60hI-60hNI	1.53133	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)	1.11069	0.748
transgenic ySAMdc/azygous control (breaker)	0.50197	0.142
transgenic ySAMdc/azygous control (red)	1.19847	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00234	0.909

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.82873	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.99987	1
Manapal/WT (break)	0.63369	0.333
Manapal/WT (red)	0.77702	0.229