El conjunto original de datos se encuentra en ebi.ac.uk. Corresponden a expresión celular de mismo componente de la hoja (mismo tejido) de plantas de A. thaliana de diferentes regiones del mundo. El artículo original es: 10.1105/tpc.16.00483
La lista de TF fue obtenida de "Plant Transcription Factor Database" (planttfdb.cbi.pku.edu.cn).
corto (Correlation Tool) es un paquete de R par generar redes de regulación genética basadas en correlaciones con DPI.
Los primero TFs mejor ranqueados de corto fueron:
| Regulon | TF name | NES | p.value |
|---|---|---|---|
| AT2G46680.1 | ATHB7 | 6.23 | 4.74e-10 |
| AT3G24520.1 | HSFC1 | 5.26 | 1.46e-07 |
| AT3G50650.1 | 4.86 | 1.19e-06 | |
| AT1G22190.1 | RAP2.4 | 4.49 | 7.21e−06 |
| AT2G19810.1 | ATOZF1 | 4.46 | 8.07e−06 |
| AT5G03680.1 | PETAL LOSS | 4.2 | 2.65e−05 |
| AT5G47640.1 | NF-YB2 | 4.12 | 3.77e−05 |
| AT3G61890.1 | ATHB12 | 4.11 | 3.9e−05 |
| AT3G19360.1 | −3.92 | 8.98e−05 | |
| AT2G27050.1 | EIL1 | 3.76 | 0.000169 |
Una búsqueda rápida en arabidopsis.org de estos genes se encontró esta descripción. Las imágenes corresponden al Arabidopsis eFP Browser, Abiotic Stress II.
La tabla "Regulon Overrepresentation Test" corresponde al análisis de sobrerepresentación del regulón de cada TMR (se usó la lista de todos los blancos detectados con corto) usando:
Analysis Type: PANTHER Overrepresentation Test (Released 20190711) Annotation Version and Release Date: GO Ontology database Released 2019-12-09 (GO Biological Process complete) Reference List: Arabidopsis thaliana (all genes in database). Cita: 10.1038/s41596-019-0128-8
Algunos regulones no enriquecieron ningún proceso biológico, esto puede ser porque: a) Puede ser consecuencia de que se carece de información de muchos de los genes blanco, b) También puede ser que la lista de genes blanco no tiene sentido (combina muchos genes de distintos procesos biológicos). Pero esto me parece poco probable ya que los genes que estamos obteniendo tienen el sentido biológico que esperábamos.
Other names: ARABIDOPSIS THALIANA HOMEOBOX 7, ATHB-7, ATHB7, HB-7, HOMEOBOX 7
Encodes a putative transcription factor that contains a homeodomain closely linked to a leucine zipper motif. Transcript is detected in all tissues examined. Is transcriptionally regulated in an ABA-dependent manner and may act in a signal transduction pathway which mediates a drought response.
ATHB7 Arabidopsis eFP Browser, Abiotic Stress II
ATHB7 Regulon Overrepresentation Test
Other names: AT-HSFC1, HEAT SHOCK TRANSCRIPTION FACTOR C1, HSFC1
member of Heat Stress Transcription Factor (Hsf) family
HSFC1 Arabidopsis eFP Browser, Abiotic Stress II
HSFC1 Regulon Overrepresentation Test
GRAS family transcription factor;(source:Araport11)
AT3G50650 Arabidopsis eFP Browser, Abiotic Stress II
AT3G50650 Regulon Overrepresentation Test
Other names: RAP2.4, RAP2.4D, RELATED TO AP2 4, RELATED TO AP2.4D, WIND2
The gene encodes a putative transcription factor belongings to the abiotic stress-associated DREB A-6 clade. The mRNA is cell-to-cell mobile.
RAP2.4 Arabidopsis eFP Browser, Abiotic Stress II
RAP2.4 Regulon Overrepresentation Test
Other names: ATOZF1, ATTZF2, OXIDATION-RELATED ZINC FINGER 1, OZF1, TANDEM ZINC FINGER 2, TZF2
Encodes Oxidation-related Zinc Finger 1 (OZF1), a plasma membrane protein involved in oxidative stress.
ATOZF1 Arabidopsis eFP Browser, Abiotic Stress II
ATOZF1 Regulon Overrepresentation Test
Other names: PETAL LOSS, PTL
Recessive mutations are defective in organ initiation and orientation in the second whorl. This gene encodes a trihelix transcription factor whose expression is limited to margins of floral and vegetative organs. Overexpression and double mutant analyses suggest that this gene is involved in limiting lateral growth of organs.
PETAL LOSS Arabidopsis eFP Browser, Abiotic Stress II
PETAL LOSS Regulon Overrepresentation Test
Other names: "NUCLEAR FACTOR Y, SUBUNIT B2", NF-YB2
Involved in the regulation of response to nutrient levels.
NF-YB2 Arabidopsis eFP Browser, Abiotic Stress II
NF-YB2 Regulon Overrepresentation Test
Other names: ARABIDOPSIS THALIANA HOMEOBOX 12, ATHB-12, ATHB12, HB-12, HB12, HOMEOBOX 12
Encodes a homeodomain leucine zipper class I (HD-Zip I) protein. Loss of function mutant has abnormally shaped leaves and stems.
ATHB12 Arabidopsis eFP Browser, Abiotic Stress II
ATHB12 Regulon Overrepresentation Test
Other names:
Zinc finger (CCCH-type) family protein;(source:Araport11)
AT3G19360.1 Arabidopsis eFP Browser, Abiotic Stress II
AT3G19360.1 Regulon Overrepresentation Test
Other names: ATEIL1, EIL1, ETHYLENE-INSENSITIVE3-LIKE 1
ethylene-insensitive3-like1 (EIL1) The mRNA is cell-to-cell mobile.
EIL1 Arabidopsis eFP Browser, Abiotic Stress II
EIL1 Regulon Overrepresentation Test
