Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.14.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85796	0.413
27DAP/17DAP	0.94469	0.863
39DAP/27DAP	0.9241	0.631
41DAP/39DAP	1.68359	0.293
42DAP/41DAP	1.21323	0.825
43DAP/42DAP	0.77637	0.589
47DAP/43DAP	0.87606	0.599
52DAP/47DAP	1.53871	0.397
57DAP/52DAP	0.69133	0.503

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02104	0.928
17DAP/reference	0.97277	0.321
27DAP/reference	0.99659	0.867
39DAP/reference	0.99072	0.828
41DAP/reference	0.93216	0.201
42DAP/reference	0.92846	0.04
43DAP/reference	0.943	0.394
47DAP/reference	0.86617	0.002
52DAP/reference	0.8831	0.065
57DAP/reference	0.89159	0.131

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9549	0.644
27DAP/17DAP	0.94078	0.782
39DAP/27DAP	1.14654	0.32
41DAP/39DAP	0.85583	0.333
42DAP/41DAP	1.04146	0.999
43DAP/42DAP	1.3594	0.025
47DAP/43DAP	1.02726	0.926
52DAP/47DAP	0.9359	0.753
57DAP/52DAP	0.95618	0.584
57DAP/7DAP	1.02148	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93213	0.296
17DAP/reference	0.94464	0.094
27DAP/reference	0.91776	0.016
39DAP/reference	0.83783	0.011
41DAP/reference	0.93901	0.284
42DAP/reference	0.81876	0.014
43DAP/reference	0.83615	0.037
47DAP/reference	0.91152	0.383
52DAP/reference	0.7907	0.033
57DAP/reference	0.80193	0.014

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01353	0.943
17DAP/reference	1.06212	0.824
27DAP/reference	1.01227	1
39DAP/reference	0.97284	0.485
41DAP/reference	0.99407	0.557
42DAP/reference	0.92452	0.169
43DAP/reference	1.15789	0.276
47DAP/reference	0.99638	0.714
52DAP/reference	0.94092	0.259
57DAP/reference	1.13104	0.324

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91808	0.092
17DAP/reference	0.9842	0.647
27DAP/reference	0.86967	0.089
39DAP/reference	0.94408	0.393
41DAP/reference	1.02348	0.826
42DAP/reference	0.88769	0.071
43DAP/reference	0.86018	0.084
47DAP/reference	1.08594	0.081
52DAP/reference	0.8938	0.334
57DAP/reference	0.74521	0.032

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.28972	0.56
26DAP/20DAP	0.94678	1
34DAP/26DAP	0.96838	0.927
51DAP/34DAP	0.98767	0.893
52DAP/51DAP	1.13189	0.207
53DAP/52DAP	1.04179	0.83
55DAP/53DAP	1.16222	0.566
57DAP/55DAP	1.06756	0.626
62DAP/57DAP	1.14716	0.393
68DAP/62DAP	1.12105	0.831
68DAP/14DAP	1.21224	0.714

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96271	0.493

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.67668	0.251
Mature Green Tomato/Ripe Tomato	0.73177	0.107
Immature Eggplant/Mature Eggplant	1.27756	0.058
Ripe Pepper/Ripe Tomato	0.85447	1
Mature Eggplant/Ripe Tomato	0.87247	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.0926	0.486
1-1-2/M82	0.9253	1
12-2/M82	1.06143	1
12-4/M82	1.04423	1
1-3/M82	0.988	1
2-1-1/M82	1.00029	1
2-1/M82	N/A	N/A
2-6/M82	0.91764	0.501
3-2/M82	1.02334
4-1-1/M82	1.05267	1
4-1/M82	0.87321	1
4-3-2/M82	0.86832	1
4-3/M82	0.77976	0.611
5-3/M82	0.96146	0.642
6-2/M82	0.90004	0.497
6-3/M82	1.03142	1
7-1/M82	N/A	N/A
7-2/M82	1.17065	1
9-3-2/M82	1.15531	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.61279	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.00612	1
IL12-4/WTpooled	0.97402	1
IL1-4/WTpooled	1.07614
WT/WTpooled	1.08445	0.85

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	1.03286	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.96051	1
DC3000/delta hrp 6h	0.78138	0.926
DC3000/delta hrp 12h	1.19753	1
DC3000/delta hrp 24h	0.94142	0.618

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.65456	0.025
DC3000 delta B/DC3000 delta AB	1.02985	0.646

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	0.95239	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0404	1
Var 0h	19.9673	0.98
Var 12h I row2-row1	1.06373	0.473
Var 12h NI row2-row1	0.91798	0.82
Var 36h I row2-row1	0.71582	0.805
Var 36h NI row2-row1	1.18599	1
Var 60h I row2-row1	1.20262	0.562
Var 60h NI row2-row1	1.0697	0.904
Time course 0hI-0hNI	1.00804	1
Time course 12hI-12hNI	1.01233	0.867
Time course 36hI-36hNI	0.98617	0.632
Time course 60hI-60hNI	1.19191	0.033

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)	0.87523	0.315
transgenic ySAMdc/azygous control (breaker)	0.85944	0.173
transgenic ySAMdc/azygous control (red)	1.08392	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.04376	0.204

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14168	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00349	1
Manapal/WT (break)	0.87379	1
Manapal/WT (red)	0.90291	0.607