Supplemental Material for Perez, 2024

Supplemental Material for Perez, 2024

<p>Tables S3 & S5 for Perez 2024. <em>Cel</em>EsT and max<em>Cel</em>EsT networks with annotations. These table (sheet 2 imported into R or Python) can be used directly with the decoupleR/decoupler package ('source' refers to TF and 'target' refe...

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التفاصيل البيبلوغرافية
المؤلف الرئيسي:	Marcos Francisco Perez (11788328) (author)
منشور في:	2024
الموضوعات:	Biological network analysis Genomics and transcriptomics transcription factor TF activity C. elegans RNA-seq gene ontology
الوسوم:	إضافة وسم لا توجد وسوم, كن أول من يضع وسما على هذه التسجيلة!

مواد مشابهة

<b>Gene ontology enrichment analysis of statistically significant differentially expressed genes (DEGs) mapped to functional biological pathways identified in the RNA-seq comparisons of WT and Ag</b><sup><strong>T</strong></sup><b> </b><b><i>A. baumannii</i></b><b> ATCC 19606.</b>
حسب: Oliver McNeilly (18715834)
منشور في: (2025)

<b>Gene ontology enrichment analysis of statistically significant differentially expressed genes (DEGs) mapped to functional biological pathways identified in the RNA-seq comparisons of WT and NAg</b><sup><strong>R</strong></sup><b> </b><b><i>A. baumannii</i></b><b> ATCC 19606.</b>
حسب: Oliver McNeilly (18715834)
منشور في: (2025)

Supplementary File 1
حسب: Kinsey Fisher (22772279)
منشور في: (2025)

Laver_et_al_2024_FilesS1_and_S3
حسب: John Calarco (20135136)
منشور في: (2024)

Exploring shared pathogenesis of multiple myeloma and osteoporosis via bioinformatic analysis
حسب: Yajie Wang (184298)
منشور في: (2025)

Binding to <i>in vivo-</i>targeted nucleosomes.
حسب: Maria Tsompana (3037167)
منشور في: (2025)

Binding to <i>in vivo</i>-targeted nucleosomes.
حسب: Maria Tsompana (3037167)
منشور في: (2025)

KLF4 binds an alternative TFBS.
حسب: Maria Tsompana (3037167)
منشور في: (2025)

TF binding to 5S and MMTV nucleosomes.
حسب: Maria Tsompana (3037167)
منشور في: (2025)

TF binding to the Widom 601 nucleosome.
حسب: Maria Tsompana (3037167)
منشور في: (2025)

Overview of Pioneer-seq.
حسب: Maria Tsompana (3037167)
منشور في: (2025)

Information on ITNs.
حسب: Maria Tsompana (3037167)
منشور في: (2025)

Table 1_Global analysis of transcription factors using both the reference genome and the multi-transcriptome of Akebia trifoliata reveals a sophisticated functional strategy.xlsx
حسب: Hao Yang (328526)
منشور في: (2025)

Data Archive: The<i> </i><i>C. elegans</i> Glutamate Transporters GLT-4 and GLT-5 Regulate Protein Expression, Behavior, and Lifespan
حسب: Grace Bronstone (20543372)
منشور في: (2025)

Supplemental Material for Dinneen <i>et al</i>., 2025
حسب: Erica Dinneen (21881798)
منشور في: (2025)

Iron-sensitive RNA regulation by poly C binding proteins
حسب: Grant A Goda (20509866)
منشور في: (2025)

Table 1_Behavioral and molecular effects of micro and nanoplastics across three plastic types in fish: weathered microfibers induce a similar response to nanosized particles.docx
حسب: Sara J. Hutton (13239009)
منشور في: (2024)

Summary of the available evidence for the physical association of nuclear TFs with the mitochondrial genome. All TFs with ChIP-seq evidence for chrM occupancy are listed in the “any” column. “BPNet confirmed” indicates that the observed ChIP-Seq pattern is corroborated in its key aspects by BPNet models. The “discordant” TFs are those for which not all available ChIP-seq experiments show chrM peaks.
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ARID1B (ARID/BRIGHT) (B) TFAP2C (AP-2); (C) C11orf30; (D) ATM.
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) MEIS2 (Homeodomain); (B) PKNOX1 (Homeodomain); (C) CUX1 (Homeodomain); (D) E2F1 (E2F).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) NFKB2 (Rel); (B) RXRA (nuclear receptor); (C) RUNX3 (Runt); (D) HSF1 (HSF).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ZNF768 (C2H2 ZNF); (B) ZNF839 (C2H2 ZNF); (C) ZNF891 (C2H2 ZNF); (D) THAP9 (THAP finger).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ZNF274 (C2H2 ZNF); (B) ZNF280B (C2H2 ZNF); (C) ZNF350 (C2H2 ZNF); (D) ZNF598 (C2H2 ZNF).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) DZIP1 (C2H2 ZNF); (B) HIVEP1 (C2H2 ZNF); (C) ZNF225 (C2H2 ZNF); (D) ZNF263 (C2H2 ZNF).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) RFX5 (RFX); (B) FOXA1 (Forkhead); (C) FOXA2 (Forkhead); (D) ZNF316 (C2H2 ZNF).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) MAX (bHLH); (B) MITF (bHLH); (C) SREBF1 (bHLH); (D) RFX1 (RFX).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) NFE2L1 (bZIP); (B) NFE2L2 (bZIP); (C) NRL (bZIP); (D) BHLHE40 (bHLH).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) MAFF (bZIP); (B) MAFG (bZIP); (C) MAFK (bZIP); (D) NFE2 (bZIP).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) CEBPB (bZIP); (B) CEBPG (bZIP); (C) JUN (bZIP); (D) JUND (bZIP).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) CREB1 (bZIP); (B) FOS (bZIP); (C) FOSL1 (bZIP); (D) FOSL2 (bZIP).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Evidence for mitochondrial genome occupancy by nuclear transcription factors. Black and yellow tracks show the forward- and reverse-strand ChIP-seq coverage over chrM. (A) ATF2 (bZIP); (B) ATF3 (bZIP); (C) ATF4 (bZIP); (D) ATF7 (bZIP).
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Global assessment of the evidence for association of human nuclear TFs with the mitochondrial genome. (A) Summary of the known human TFs and available ENCODE TF ChIP datasets. The TF classification of human TFs of Lambert et al. 2018 [1] was followed. (B) Hierarchical clustering of ChIP-seq profiles over the mitochondrial genome for 6,513 TF ChIP-seq datasets. Datasets that show evidence for non-artefactual association with mitochondrial DNA are highlighted at the bottom.
حسب: Georgi K Marinov (2863319)
منشور في: (2025)

Supplementary Material
حسب: Waqasuddin Khan (5009642)
منشور في: (2024)

Identification of prognostic burns-related indicators and microRNA biosignatures in burns patients with inhalation injury
حسب: Tarryn Prinsloo (22619858)
منشور في: (2025)

Supplemental figures S1-S4.pdf
حسب: Young Chul Kim (14100963)
منشور في: (2024)

Suppl material "<b>An atlas of thyroid hormone responsive genes in adult mouse hypothalamus</b>" Wu et al Endocrinology 2025
حسب: Frederic Flamant (12510451)
منشور في: (2025)

Data to reproduce figures in RNAdecayCafe paper
حسب: Isaac Vock (20932472)
منشور في: (2025)

The function of hub genes from GeneCards database.
حسب: Wen-tao Zhang (19959271)
منشور في: (2024)

GSEA analysis of DEGs.
حسب: Wen-tao Zhang (19959271)
منشور في: (2024)

The top 10 terms in KEGG analysis of 57 DE-PRGs in CKD.
حسب: Wen-tao Zhang (19959271)
منشور في: (2024)

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