Classification of enhancer promoter interaction pairs based on expression patterns and distances involved in disease manifestation in human
Notice bibliographique
Résumé
Enhancers-the non-coding regions of genomes' are responsible for regulation of transcription of interacting genes. In different cell lines different regions act as enhancers. Enhancer-promoter interaction (EPI) models suggest that enhancer helps in the assembly of transcription factors along with RNA polymerase II and interacts with promoters to increase the expression of corresponding genes. During transcription, enhancer itself undergoes transcription giving rise to small RNAs, known as enhancer RNA. Presence of Transcription Start Sites (TSS) in annotated enhancer regions is also defined as active enhancers. Three different human cell-lines namely, Gm12878, K562 and H1-hesc which are normal, cancerous and stem cell-lines respectively were studied. K-medoids algorithm was used to segregate EPI in all the cell-lines. Three clusters were derived on the basis of expression of enhancer, expression of their interacting promoters and distance between the two. Statistical t-test analysis showed that all clusters were different from each other. Cluster-1 (expression of enhancer Mean (eeMean) =59.12, Median (eeMedian) =12.09) and cluster-2 (eeMean=1799.9, eeMedian=1468) differ from each other on the basis of enhancer's expression. Cluster-2 (distance mean=20521, eeMean=1799.9; distance median=7984, eeMedian=1468.5) was different from cluster-3 (distance mean=180798, distance median=162626) on the basis of distance and the expression of TSS at enhancer. Finally cluster-1 (distance mean=18030, distance median=6966) and cluster-3 (distance mean=180798, distance median=162626) differ from each other on the basis of distance. RNAseq analysis showed 7 upregulated genes in K562 compared to Gm12878. Further, EPI distributions of MYC, RAD23B and Insulin like growth factors showed similar pattern in K562 and H1hesc, and they were present in cluster-1. Whereas EPI of MDN1, CDKN1C, and eukaryotic translation elongation factor2 in K562 were present in cluster-1 and EPI of H1hesc were present in cluster-1 and cluster-3. EPI of Erythrocyte membrane protein were segregated into cluster-1 and cluster-3 for both K562 and H1hesc, whereas all of these interactions were absent in Gm12878. Overall these results suggests that enhancer activities are mainly responsible for carcinogenesis in K562 cell-lines otherwise absent in normal cell-lines.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».