Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.13.9

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07964	0.838
27DAP/17DAP	0.94979	0.913
39DAP/27DAP	0.99253	0.749
41DAP/39DAP	1.42759	0.603
42DAP/41DAP	0.97368	1
43DAP/42DAP	0.94949	0.887
47DAP/43DAP	0.93778	0.693
52DAP/47DAP	1.35699	0.474
57DAP/52DAP	0.87261	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93853	0.284
17DAP/reference	0.89496	0.028
27DAP/reference	1.02099	0.806
39DAP/reference	0.96427	0.575
41DAP/reference	0.9455	0.434
42DAP/reference	0.9074	0.024
43DAP/reference	0.95561	0.538
47DAP/reference	0.90116	0.035
52DAP/reference	0.99543	0.636
57DAP/reference	1.06633	0.153

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07252	0.719
27DAP/17DAP	0.98037	0.919
39DAP/27DAP	1.08121	0.685
41DAP/39DAP	1.02455	1
42DAP/41DAP	0.78318	0.048
43DAP/42DAP	1.09124	0.478
47DAP/43DAP	1.05157	0.914
52DAP/47DAP	0.94828	0.807
57DAP/52DAP	1.03803	1
57DAP/7DAP	0.82923	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78005	0.086
17DAP/reference	0.823	0.039
27DAP/reference	0.88608	0.042
39DAP/reference	0.80127	0.039
41DAP/reference	0.79469	0.023
42DAP/reference	0.81554	0.013
43DAP/reference	0.86173	0.23
47DAP/reference	0.82545	0.057
52DAP/reference	0.77102	0.022
57DAP/reference	0.79466	0.019

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95426	0.592
17DAP/reference	0.92423	0.297
27DAP/reference	0.90068	0.173
39DAP/reference	0.84713	0.072
41DAP/reference	0.97966	0.493
42DAP/reference	0.99943	0.655
43DAP/reference	1.23123	0.128
47DAP/reference	1.11801	0.291
52DAP/reference	0.908	0.086
57DAP/reference	0.94083	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83592	0.045
17DAP/reference	0.9412	0.462
27DAP/reference	0.86708	0.058
39DAP/reference	0.90164	0.111
41DAP/reference	0.89728	0.209
42DAP/reference	0.93709	0.22
43DAP/reference	0.78438	0.023
47DAP/reference	0.9844	0.558
52DAP/reference	0.8626	0.139
57DAP/reference	1.07686	0.614

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06129	0.966
26DAP/20DAP	0.72324	0.244
34DAP/26DAP	1.124	0.819
51DAP/34DAP	0.95138	0.807
52DAP/51DAP	1.18796	0.253
53DAP/52DAP	0.96364	0.824
55DAP/53DAP	0.98966	0.876
57DAP/55DAP	1.12067	0.841
62DAP/57DAP	1.28866	0.393
68DAP/62DAP	0.9922	0.885
68DAP/14DAP	1.22958	0.153

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.85583	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.06302	0.267
Immature Eggplant/Mature Eggplant	N/A	N/A
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	1.08354	1
1-1-2/M82	0.87763	1
12-2/M82	1.57321	0.405
12-4/M82	0.88297	1
1-3/M82	0.95265	1
2-1-1/M82	0.63867
2-1/M82	N/A	N/A
2-6/M82	1.04401	1
3-2/M82	0.69905
4-1-1/M82	0.87876	1
4-1/M82	1.1916	1
4-3-2/M82	0.84418	0.698
4-3/M82	0.85659	1
5-3/M82	0.90439	0.642
6-2/M82	0.75934	0.497
6-3/M82	0.90795	0.982
7-1/M82	1.00591	1
7-2/M82	1.09654	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.95634	1
IL12-4/WTpooled	1.06555
IL1-4/WTpooled	0.82738
WT/WTpooled	1.2749	0.874

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	0.88497	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07655	0.875
DC3000/delta hrp 6h	1.11362	1
DC3000/delta hrp 12h	1.19814	1
DC3000/delta hrp 24h	0.97398	0.84

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.09408

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.08929	1
Exp 36h	0.65303	0.504
Exp 60h	0.55316	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.94837	1
Var 0h	1.05569	1
Var 12h I row2-row1	1.1043	0.406
Var 12h NI row2-row1	0.83287	0.494
Var 36h I row2-row1	0.84552	1
Var 36h NI row2-row1	0.90142	0.469
Var 60h I row2-row1	1.24861	0.562
Var 60h NI row2-row1	1.14906	0.904
Time course 0hI-0hNI	1.04256	0.833
Time course 12hI-12hNI	0.91436	0.255
Time course 36hI-36hNI	0.8335	0.034
Time course 60hI-60hNI	0.67893	0.047

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)	2.21754	0.272
transgenic ySAMdc/azygous control (breaker)	2.99258	0.248
transgenic ySAMdc/azygous control (red)	0.98447	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00128	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.2918	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.86916	0.093
Manapal/WT (break)	1.29292	1
Manapal/WT (red)	1.13848	1