Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.7.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.42031	0.303
27DAP/17DAP	0.4974	0.03
39DAP/27DAP	0.95845	0.583
41DAP/39DAP	0.48987	0.041
42DAP/41DAP	0.83084	1
43DAP/42DAP	1.14739	0.906
47DAP/43DAP	0.50163	0.049
52DAP/47DAP	0.92765	0.779
57DAP/52DAP	0.93185	0.923

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15284	0.872
17DAP/reference	0.88581	0.18
27DAP/reference	0.83704	0.013
39DAP/reference	0.74325	0.085
41DAP/reference	0.96836	0.814
42DAP/reference	1.16443	0.05
43DAP/reference	0.98635	0.763
47DAP/reference	1.07126	0.329
52DAP/reference	1.23747	0.167
57DAP/reference	1.14513	0.321

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.851	0.388
27DAP/17DAP	1.15009	0.768
39DAP/27DAP	1.11243	0.691
41DAP/39DAP	0.9272	0.849
42DAP/41DAP	1.13658	0.508
43DAP/42DAP	0.68042	0.024
47DAP/43DAP	1.01258	0.923
52DAP/47DAP	3.11346
57DAP/52DAP	1.78841	0.084
57DAP/7DAP	3.62445	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.09533	0.286
17DAP/reference	1.3263	0.006
27DAP/reference	1.40049	0.009
39DAP/reference	1.04798	0.634
41DAP/reference	1.17431
42DAP/reference	1.35728
43DAP/reference	1.40749	0.307
47DAP/reference	0.87087
52DAP/reference	1.21314	0.062
57DAP/reference	1.46287	0.003

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80964
17DAP/reference	0.96444	0.077
27DAP/reference	1.01166	1
39DAP/reference	1.16757	0.097
41DAP/reference	1.02073	1
42DAP/reference	1.05731	0.715
43DAP/reference	0.82364	0.08
47DAP/reference	0.97259	0.368
52DAP/reference	1.16062	0.014
57DAP/reference	1.09574	0.252

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12602	0.23
17DAP/reference	1.02032	1
27DAP/reference	1.69716	0.02
39DAP/reference	1.41015	0.075
41DAP/reference	1.27817	0.012
42DAP/reference	1.52441	0.013
43DAP/reference	1.38095	0.007
47DAP/reference	1.03045	1
52DAP/reference	1.40325
57DAP/reference	1.97781	0.023

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.10743	0.966
26DAP/20DAP	3.64899	0.683
34DAP/26DAP	1.69243	1
51DAP/34DAP	0.97877
52DAP/51DAP	5.13125	0.034
53DAP/52DAP	0.71238	0.167
55DAP/53DAP	N/A	N/A
57DAP/55DAP	0.21642	0.059
62DAP/57DAP	1.47862	0.133
68DAP/62DAP	1.71968
68DAP/14DAP	2.49452	0.061

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.19326	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	3.74598	0.058
Mature Green Tomato/Ripe Tomato	15.5699	0.015
Immature Eggplant/Mature Eggplant	0.40529	0.057
Ripe Pepper/Ripe Tomato	39.3545	0.256
Mature Eggplant/Ripe Tomato	65.558	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	1.01369
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	0.98647
3-2/M82	N/A	N/A
4-1-1/M82	0.98209
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.55079
5-3/M82	1.47683	0.496
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.11637
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.20145	0.493
IL2-6/WTpooled	1.32926	0.584
IL7-5/WTpooled	0.70206	1
IL7-3/WTpooled	0.82545	0.418
IL12-4/WTpooled	1.16608	0.891
IL1-4/WTpooled	0.72831	0.402
WT/WTpooled	1.03132	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	0.99458	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.97603	1
DC3000/delta hrp 6h	0.9449	0.95
DC3000/delta hrp 12h	1.02095	1
DC3000/delta hrp 24h	0.96112	0.75

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86767	0.213
DC3000 delta B/DC3000 delta AB	0.86231	0.11

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	0.9921	1
Var 0h	1.69019	0.782
Var 12h I row2-row1	0.86828	0.363
Var 12h NI row2-row1	1.00398	1
Var 36h I row2-row1	0.85611	0.805
Var 36h NI row2-row1	1.05946	1
Var 60h I row2-row1	0.99669	1
Var 60h NI row2-row1	0.99306	1
Time course 0hI-0hNI	0.98862	0.999
Time course 12hI-12hNI	1.06613	0.544
Time course 36hI-36hNI	0.96464	0.373
Time course 60hI-60hNI	0.46138	0.007

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)	1.08771	0.798
transgenic ySAMdc/azygous control (breaker)	3.88713	0.162
transgenic ySAMdc/azygous control (red)	1.11561	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.4616	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.47459	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	30.4908	0.09
Manapal/WT (break)	12.004	0.123
Manapal/WT (red)	2.35604	0.413