Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.8.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01508	0.891
27DAP/17DAP	1.0847	0.868
39DAP/27DAP	0.85642	0.402
41DAP/39DAP	1.66274	0.118
42DAP/41DAP	1.00846	1
43DAP/42DAP	0.99	0.93
47DAP/43DAP	1.07627	0.926
52DAP/47DAP	1.44365	0.346
57DAP/52DAP	0.87996	0.759

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.90087	0.121
17DAP/reference	1.13758	0.096
27DAP/reference	0.97377	0.61
39DAP/reference	1.03367	0.734
41DAP/reference	0.98699	0.814
42DAP/reference	0.91238	0.04
43DAP/reference	1.04577	0.425
47DAP/reference	0.90332	0.116
52DAP/reference	0.96838	0.36
57DAP/reference	1.11285	0.405

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.16127	0.975
27DAP/17DAP	0.94269	0.821
39DAP/27DAP	1.04398	0.793
41DAP/39DAP	1.07736	0.79
42DAP/41DAP	1.1094	0.984
43DAP/42DAP	0.93486	0.321
47DAP/43DAP	0.92758	0.41
52DAP/47DAP	1.17264	0.498
57DAP/52DAP	1.0538	1
57DAP/7DAP	1.27531	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80934	0.077
17DAP/reference	0.84214	0.072
27DAP/reference	0.97551	0.43
39DAP/reference	0.95379	0.354
41DAP/reference	0.89782	0.213
42DAP/reference	0.7184	0.07
43DAP/reference	0.85712	0.159
47DAP/reference	0.91483	0.383
52DAP/reference	0.82742	0.09
57DAP/reference	0.83791	0.043

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06016	0.75
17DAP/reference	0.86381	0.153
27DAP/reference	0.93867	0.393
39DAP/reference	0.87184	0.099
41DAP/reference	0.97844	0.459
42DAP/reference	0.89646	0.098
43DAP/reference	1.26335	0.086
47DAP/reference	0.98903	0.609
52DAP/reference	1.08371	0.747
57DAP/reference	1.00839	0.834

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95605	0.422
17DAP/reference	1.04327	0.638
27DAP/reference	0.97021	0.566
39DAP/reference	1.12977	0.691
41DAP/reference	0.93544	0.331
42DAP/reference	0.88239	0.059
43DAP/reference	0.87921	0.256
47DAP/reference	1.08998	0.196
52DAP/reference	0.91603	0.444
57DAP/reference	1.31059	0.285

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00232	1
26DAP/20DAP	0.8531	0.317
34DAP/26DAP	0.89819	0.763
51DAP/34DAP	0.93197	0.674
52DAP/51DAP	1.19326	0.271
53DAP/52DAP	0.99548	0.978
55DAP/53DAP	1.03218	0.927
57DAP/55DAP	0.8709	0.539
62DAP/57DAP	1.20921	0.678
68DAP/62DAP	1.04779	1
68DAP/14DAP	0.74973	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.79337	0.036

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.81602	0.079
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.45696
Mature Eggplant/Ripe Tomato	0.72458	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96223	0.883
1-1-2/M82	0.95219
12-2/M82	1.12984
12-4/M82	1.07844	1
1-3/M82	0.5411	0.376
2-1-1/M82	0.93882
2-1/M82	N/A	N/A
2-6/M82	0.93142	1
3-2/M82	N/A	N/A
4-1-1/M82	1.15319
4-1/M82	1.21658
4-3-2/M82	0.90317
4-3/M82	1.13143
5-3/M82	0.96212	1
6-2/M82	0.77916
6-3/M82	0.7659	1
7-1/M82	N/A	N/A
7-2/M82	0.94047	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	0.97663	1
IL7-5/WTpooled	0.68973
IL7-3/WTpooled	0.87091	1
IL12-4/WTpooled	0.80236	0.71
IL1-4/WTpooled	1.07153
WT/WTpooled	0.98526	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	0.8658	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07671	0.921
DC3000/delta hrp 6h	1.25956	0.95
DC3000/delta hrp 12h	1.25451	1
DC3000/delta hrp 24h	1.11161	0.308

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.78914	0.065
DC3000 delta B/DC3000 delta AB	0.97815	0.873

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95407	1
Var 0h	1.03411	1
Var 12h I row2-row1	0.82527	0.418
Var 12h NI row2-row1	1.06184	1
Var 36h I row2-row1	0.76651	1
Var 36h NI row2-row1	1.6293	0.482
Var 60h I row2-row1	1.01765	1
Var 60h NI row2-row1	0.97035	1
Time course 0hI-0hNI	0.97965	0.936
Time course 12hI-12hNI	0.99256	0.984
Time course 36hI-36hNI	0.90618	0.127
Time course 60hI-60hNI	0.24952	0.005

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)	0.95057	0.614
transgenic ySAMdc/azygous control (breaker)	0.78364	0.131
transgenic ySAMdc/azygous control (red)	0.92768	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.96933	0.095

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.90887	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.79047	1
Manapal/WT (break)	0.8915	1
Manapal/WT (red)	0.64274	0.181