Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.4.11.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.95646	0.671
27DAP/17DAP	1.05373	1
39DAP/27DAP	1.00683	0.857
41DAP/39DAP	1.60899	0.153
42DAP/41DAP	1.00278	1
43DAP/42DAP	1.01735	0.937
47DAP/43DAP	0.89672	0.64
52DAP/47DAP	1.18492	0.821
57DAP/52DAP	1.09443	0.969

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.59936
17DAP/reference	0.74001	0.18
27DAP/reference	0.97559
39DAP/reference	0.54896
41DAP/reference	0.63842
42DAP/reference	0.34988
43DAP/reference	0.97438	0.861
47DAP/reference	1.33472
52DAP/reference	N/A	N/A
57DAP/reference	N/A	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94731	0.629
27DAP/17DAP	0.99004	0.969
39DAP/27DAP	1.18097	0.378
41DAP/39DAP	0.83525	0.096
42DAP/41DAP	1.35547	0.005
43DAP/42DAP	0.91234	0.308
47DAP/43DAP	1.04062	0.906
52DAP/47DAP	1.0524	0.862
57DAP/52DAP	0.8942	0.505
57DAP/7DAP	1.04348	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.44909	0.024
17DAP/reference	1.43446	0.01
27DAP/reference	2.02642	0.007
39DAP/reference	1.77237	0.008
41DAP/reference	2.29901	0.008
42DAP/reference	2.01497	0.03
43DAP/reference	2.72166	0.008
47DAP/reference	2.75532	0.028
52DAP/reference	10.1638	0.007
57DAP/reference	7.4261	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.86326	0.669
17DAP/reference	0.27475
27DAP/reference	N/A	N/A
39DAP/reference	N/A	N/A
41DAP/reference	N/A	N/A
42DAP/reference	3.39291
43DAP/reference	0.88638	0.478
47DAP/reference	1.46528
52DAP/reference	1.8374	0.208
57DAP/reference	N/A	N/A

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.96323	0.015
17DAP/reference	1.10723	0.212
27DAP/reference	1.6926	0.02
39DAP/reference	4.77174	0.009
41DAP/reference	3.33612	0.006
42DAP/reference	1.8295	0.016
43DAP/reference	1.85029	0.021
47DAP/reference	0.71069
52DAP/reference	2.94888	0.03
57DAP/reference	4.99037

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97615	1
26DAP/20DAP	0.6389	0.119
34DAP/26DAP	0.94177	0.898
51DAP/34DAP	0.95404	0.791
52DAP/51DAP	1.18767	0.367
53DAP/52DAP	1.01659	0.91
55DAP/53DAP	1.05028	1
57DAP/55DAP	1.16092	0.955
62DAP/57DAP	1.14676	0.8
68DAP/62DAP	1.25975	0.375
68DAP/14DAP	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.10268	0.439

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81256	0.268
Mature Green Tomato/Ripe Tomato	1.28622	0.166
Immature Eggplant/Mature Eggplant	1.34245	0.066
Ripe Pepper/Ripe Tomato	1.18003	1
Mature Eggplant/Ripe Tomato	0.84466	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.34999
1-1-2/M82	0.88917	1
12-2/M82	0.75363
12-4/M82	0.77124	0.358
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	1.22557
3-2/M82	1.32688	0.967
4-1-1/M82	N/A	N/A
4-1/M82	0.96265	1
4-3-2/M82	0.75418	0.698
4-3/M82	1.04468	1
5-3/M82	1.12344	1
6-2/M82	N/A	N/A
6-3/M82	0.77901
7-1/M82	0.91023	0.452
7-2/M82	1.40415	0.385
9-3-2/M82	0.87255	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06784	0.493
IL2-6/WTpooled	0.88648	1
IL7-5/WTpooled	0.90947	1
IL7-3/WTpooled	0.94831	1
IL12-4/WTpooled	1.13421	0.695
IL1-4/WTpooled	0.96316	0.834
WT/WTpooled	1.04234	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	1.07455	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.81422	1
DC3000/delta hrp 6h	0.96937	0.95
DC3000/delta hrp 12h	1.12999	1
DC3000/delta hrp 24h	1.30922	0.296

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.53731	0.081
DC3000 delta B/DC3000 delta AB	1.16739	0.259

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00424	1
Exp 36h	0.98661	1
Exp 60h	0.99676	1

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

hybridization	ratio	FDR (corrected p value)
self-self	0.96966	1
Var 0h	0.72598	1
Var 12h I row2-row1	1.21236	0.208
Var 12h NI row2-row1	0.79746	0.466
Var 36h I row2-row1	1.04862	1
Var 36h NI row2-row1	1.12821	1
Var 60h I row2-row1	1.43587	1
Var 60h NI row2-row1	1.22401	0.904
Time course 0hI-0hNI	1.10774	0.852
Time course 12hI-12hNI	1.02237	0.85
Time course 36hI-36hNI	0.92865	0.352
Time course 60hI-60hNI	1.07282	0.495

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	N/A	N/A

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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)	0.81122	0.172
Manapal/WT (break)	0.93878	1
Manapal/WT (red)	0.85864	0.424