Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.1.12.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.96341	0.752
27DAP/17DAP	1.17957	0.842
39DAP/27DAP	1.28201	0.382
41DAP/39DAP	0.97147	0.772
42DAP/41DAP	0.98125	1
43DAP/42DAP	0.93963	0.865
47DAP/43DAP	1.0238	1
52DAP/47DAP	0.92738	0.769
57DAP/52DAP	0.90864	0.852

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8394	0.092
17DAP/reference	0.92752	0.278
27DAP/reference	0.97744	0.654
39DAP/reference	0.93896	0.324
41DAP/reference	0.77439	0.031
42DAP/reference	0.83902	0.139
43DAP/reference	0.91939	0.211
47DAP/reference	1.01012	1
52DAP/reference	0.98966	0.618
57DAP/reference	1.01665	0.853

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08273	0.605
27DAP/17DAP	1.11196	0.664
39DAP/27DAP	1.14614	0.499
41DAP/39DAP	1.07166	0.774
42DAP/41DAP	0.93043	0.529
43DAP/42DAP	1.03839	0.788
47DAP/43DAP	1.03649	0.941
52DAP/47DAP	0.98507	0.919
57DAP/52DAP	0.98816	0.813
57DAP/7DAP	1.13819	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8598	0.063
17DAP/reference	1.11807	0.244
27DAP/reference	0.96119	0.325
39DAP/reference	0.93587	0.264
41DAP/reference	0.92821	0.271
42DAP/reference	0.92333	0.037
43DAP/reference	0.88312	0.132
47DAP/reference	0.93841	0.383
52DAP/reference	0.88495	0.09
57DAP/reference	0.90367	0.144

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92813	0.487
17DAP/reference	0.9218	0.23
27DAP/reference	0.93288	0.292
39DAP/reference	0.92557	0.322
41DAP/reference	0.85968	0.11
42DAP/reference	1.03853	0.969
43DAP/reference	0.76195	0.007
47DAP/reference	0.87542	0.053
52DAP/reference	0.79335	0.018
57DAP/reference	0.69936	0.107

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06667	0.469
17DAP/reference	0.87981	0.063
27DAP/reference	1.08235	0.487
39DAP/reference	1.05255	0.275
41DAP/reference	1.03096	0.734
42DAP/reference	1.03897	0.743
43DAP/reference	0.88183	0.046
47DAP/reference	0.8782	0.114
52DAP/reference	0.8005	0.091
57DAP/reference	1.02316	0.947

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90285	0.915
26DAP/20DAP	0.87397	0.512
34DAP/26DAP	1.04197	1
51DAP/34DAP	0.8351	0.085
52DAP/51DAP	0.9618	1
53DAP/52DAP	0.91319	0.649
55DAP/53DAP	0.988	0.864
57DAP/55DAP	0.97586	0.855
62DAP/57DAP	0.9129	0.466
68DAP/62DAP	1.17625	0.664
68DAP/14DAP	1.16366	0.615

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.7952	0.072

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.56161	0.058
Mature Green Tomato/Ripe Tomato	2.0479	0.331
Immature Eggplant/Mature Eggplant	1.14834	0.215
Ripe Pepper/Ripe Tomato	1.32073	1
Mature Eggplant/Ripe Tomato	0.93379	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01923	1
1-1-2/M82	0.85879	1
12-2/M82	1.0995	1
12-4/M82	0.79965	0.358
1-3/M82	0.81429	0.378
2-1-1/M82	0.9574	1
2-1/M82	0.91702	1
2-6/M82	0.94019	1
3-2/M82	N/A	N/A
4-1-1/M82	0.92106	1
4-1/M82	1.21481	0.853
4-3-2/M82	0.73054	0.487
4-3/M82	0.72074	0.611
5-3/M82	0.98466	1
6-2/M82	0.74533	0.497
6-3/M82	1.05819	1
7-1/M82	0.93791	1
7-2/M82	0.8896	0.599
9-3-2/M82	0.64862	0.355

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	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	N/A	N/A

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	1.09768	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01309	1
DC3000/delta hrp 6h	0.90945	0.95
DC3000/delta hrp 12h	0.97138	1
DC3000/delta hrp 24h	1.06625	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.76255
DC3000 delta B/DC3000 delta AB	1.25576

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.17218	1
Exp 36h	0.90751	0.749
Exp 60h	1.05744	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98926	1
Var 0h	0.91747	0.933
Var 12h I row2-row1	0.98025	0.856
Var 12h NI row2-row1	0.84449	1
Var 36h I row2-row1	1.02793	1
Var 36h NI row2-row1	0.89223	0.706
Var 60h I row2-row1	0.83968	0.439
Var 60h NI row2-row1	0.97258	1
Time course 0hI-0hNI	1.06036	0.662
Time course 12hI-12hNI	1.07258	0.381
Time course 36hI-36hNI	1.35722	0.006
Time course 60hI-60hNI	2.61292	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)	1.16311	0.221
transgenic ySAMdc/azygous control (breaker)	0.89945	0.49
transgenic ySAMdc/azygous control (red)	0.80181	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03428	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90131	0.308

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0186	1
Manapal/WT (break)	1.00486	1
Manapal/WT (red)	0.95225	0.607