Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73666	0.187
27DAP/17DAP	1.29548	0.809
39DAP/27DAP	1.14791	0.825
41DAP/39DAP	0.98897	0.941
42DAP/41DAP	1.05237	0.999
43DAP/42DAP	0.98852	0.914
47DAP/43DAP	1.18362	0.584
52DAP/47DAP	1.18229	0.702
57DAP/52DAP	1.06087	0.988

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92202	0.067
17DAP/reference	1.0197	0.565
27DAP/reference	1.08193	0.17
39DAP/reference	1.0336	0.603
41DAP/reference	1.10056	0.041
42DAP/reference	0.97665	0.233
43DAP/reference	1.06668	0.306
47DAP/reference	0.99753	0.674
52DAP/reference	0.94404	0.292
57DAP/reference	0.971	0.377

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04239	0.91
27DAP/17DAP	1.04489	0.932
39DAP/27DAP	1.22243	0.41
41DAP/39DAP	1.09565	0.853
42DAP/41DAP	0.92992	0.617
43DAP/42DAP	0.96906	0.751
47DAP/43DAP	1.13566	0.552
52DAP/47DAP	0.92805	0.746
57DAP/52DAP	0.85935	0.405
57DAP/7DAP	1.17856	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07326	0.65
17DAP/reference	1.14497	0.297
27DAP/reference	1.1011	0.371
39DAP/reference	1.54372	0.008
41DAP/reference	1.33364	0.03
42DAP/reference	1.28592	0.037
43DAP/reference	1.38182	0.013
47DAP/reference	1.10368	0.717
52DAP/reference	1.30705	0.015
57DAP/reference	1.17004	0.024

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03569	0.719
17DAP/reference	1.01762	0.873
27DAP/reference	1.00209	0.79
39DAP/reference	1.04853	0.912
41DAP/reference	0.89078	0.064
42DAP/reference	0.92385	0.15
43DAP/reference	1.06327	0.785
47DAP/reference	0.92255	0.064
52DAP/reference	0.95154	0.38
57DAP/reference	1.4344	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04556	0.74
17DAP/reference	1.10555	0.311
27DAP/reference	1.17432	0.149
39DAP/reference	1.19058	0.081
41DAP/reference	1.29573	0.139
42DAP/reference	1.06516	0.671
43DAP/reference	1.01936	0.894
47DAP/reference	0.89528	0.231
52DAP/reference	1.01756	0.888
57DAP/reference	0.84769	0.082

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.94847	1
26DAP/20DAP	0.89657	1
34DAP/26DAP	1.41625	0.154
51DAP/34DAP	0.97461	0.883
52DAP/51DAP	1.37508	0.454
53DAP/52DAP	1.17423	0.565
55DAP/53DAP	0.86802	0.098
57DAP/55DAP	0.93776	0.688
62DAP/57DAP	1.16557	0.8
68DAP/62DAP	0.61256	0.068
68DAP/14DAP	0.57648	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.7989	0.326

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	11.6362
Ripe Pepper/Ripe Tomato	1.16176	1
Mature Eggplant/Ripe Tomato	1.52475	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	1.06569	1
12-2/M82	1.38921
12-4/M82	0.77221	1
1-3/M82	0.99037
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.15714
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	1.27144	0.496
6-2/M82	N/A	N/A
6-3/M82	0.92062
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
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	0.80838
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83191	0.294
IL12-4/WTpooled	1.0633	0.538
IL1-4/WTpooled	1.0649	1
WT/WTpooled	0.99473	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	1.53157	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.30611	0.921
DC3000/delta hrp 6h	1.39588	0.978
DC3000/delta hrp 12h	1.07624	1
DC3000/delta hrp 24h	0.88705	0.207

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.16797	0.254
Exp 36h	1.40632	1
Exp 60h	1.21948	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03635	1
Var 0h	1.31414
Var 12h I row2-row1	1.64952	0.406
Var 12h NI row2-row1	1.11569
Var 36h I row2-row1	1.29793	1
Var 36h NI row2-row1	0.70419	0.45
Var 60h I row2-row1	0.91861	0.832
Var 60h NI row2-row1	0.88622	0.866
Time course 0hI-0hNI	1.31106	0.151
Time course 12hI-12hNI	1.13861	1
Time course 36hI-36hNI	1.99322	0.017
Time course 60hI-60hNI	2.84643	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)	0.88069	0.314
transgenic ySAMdc/azygous control (breaker)	0.91606	0.251
transgenic ySAMdc/azygous control (red)	1.00091	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00831	0.687

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)	1.47855	1
Manapal/WT (break)	1.22711	0.14
Manapal/WT (red)	0.79421	0.274