Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.11.15

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.97716	0.801
27DAP/17DAP	1.00144	1
39DAP/27DAP	1.25445	0.527
41DAP/39DAP	0.88581	0.54
42DAP/41DAP	1.04201	1
43DAP/42DAP	1.17571	0.968
47DAP/43DAP	0.79826	0.377
52DAP/47DAP	1.38122	0.545
57DAP/52DAP	1.05239	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	N/A	N/A
17DAP/reference	N/A	N/A
27DAP/reference	0.51386
39DAP/reference	2.58615	0.603
41DAP/reference	1.43265	0.029
42DAP/reference	1.67939	0.065
43DAP/reference	N/A	N/A
47DAP/reference	0.69022	0.002
52DAP/reference	1.21951	1
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00882	1
27DAP/17DAP	0.90811	0.079
39DAP/27DAP	0.88161	0.247
41DAP/39DAP	1.33606	0.69
42DAP/41DAP	0.80705	0.095
43DAP/42DAP	0.93175	0.538
47DAP/43DAP	0.96431	0.833
52DAP/47DAP	0.90896
57DAP/52DAP	0.91197	0.587
57DAP/7DAP	0.6458	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.11185	0.181
17DAP/reference	1.03481	0.477
27DAP/reference	0.99749	0.748
39DAP/reference	1.07696	0.059
41DAP/reference	0.96241	0.341
42DAP/reference	0.90861	0.013
43DAP/reference	0.9272	0.121
47DAP/reference	1.08844	0.582
52DAP/reference	0.99039	0.679
57DAP/reference	1.04002	0.183

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04394	0.397
17DAP/reference	1.09886	0.278
27DAP/reference	1.17399	0.297
39DAP/reference	1.07485	0.62
41DAP/reference	1.18609	0.657
42DAP/reference	1.11889
43DAP/reference	1.05571	0.751
47DAP/reference	N/A	N/A
52DAP/reference	0.97808	0.469
57DAP/reference	1.11404	0.037

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95436	0.074
17DAP/reference	1.00953	0.988
27DAP/reference	0.98286	0.397
39DAP/reference	0.98054	0.464
41DAP/reference	0.98426	0.512
42DAP/reference	0.91557	0.134
43DAP/reference	0.95927	0.206
47DAP/reference	0.93357	0.315
52DAP/reference	1.00467	1
57DAP/reference	0.82609	0.017

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00798	0.966
26DAP/20DAP	1.31265	0.39
34DAP/26DAP	0.92176	0.735
51DAP/34DAP	1.11735	0.445
52DAP/51DAP	1.13261
53DAP/52DAP	1.01338	0.944
55DAP/53DAP	1.05456	0.876
57DAP/55DAP	0.93645	0.694
62DAP/57DAP	1.04549	1
68DAP/62DAP	1.11151	1
68DAP/14DAP	0.83005	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.88597	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.9658	0.075
Mature Green Tomato/Ripe Tomato	1.19276	0.898
Immature Eggplant/Mature Eggplant	0.95806	1
Ripe Pepper/Ripe Tomato	0.39406	0.224
Mature Eggplant/Ripe Tomato	0.33944	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.99268	1
1-1-2/M82	1.05203	1
12-2/M82	1.05108	1
12-4/M82	1.04435	0.694
1-3/M82	1.12196	1
2-1-1/M82	1.03764	1
2-1/M82	1.22466	1
2-6/M82	1.15697	0.505
3-2/M82	0.91346	0.455
4-1-1/M82	1.03038	1
4-1/M82	0.81102	0.737
4-3-2/M82	1.06196	1
4-3/M82	0.99207	1
5-3/M82	0.97462	0.642
6-2/M82	1.06058	1
6-3/M82	1.01985	1
7-1/M82	1.02289	1
7-2/M82	1.15655	0.302
9-3-2/M82	1.03901	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.24863	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.98296	1
IL12-4/WTpooled	1.054	0.891
IL1-4/WTpooled	0.97806	0.699
WT/WTpooled	1.16222	0.911

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	1.11159	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.03879	0.914
DC3000/delta hrp 6h	1.10526	1
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.06423	0.553

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.74188	0.042
DC3000 delta B/DC3000 delta AB	1.57098	0.081

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0091	1
Exp 36h	0.91165	0.879
Exp 60h	1.04637	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02177	1
Var 0h	0.90734	0.933
Var 12h I row2-row1	1.07737	0.58
Var 12h NI row2-row1	1.14915	0.649
Var 36h I row2-row1	1.29071	0.298
Var 36h NI row2-row1	0.95939	0.791
Var 60h I row2-row1	0.90174	0.285
Var 60h NI row2-row1	0.82986	0.292
Time course 0hI-0hNI	1.0803	0.603
Time course 12hI-12hNI	1.01797	0.867
Time course 36hI-36hNI	1.37381	0.006
Time course 60hI-60hNI	4.57147	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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.55655	0.172
Manapal/WT (break)	0.85126	1
Manapal/WT (red)	0.89053	0.274