inst/update_notes/compendium_update.md

In linquynus/TFregulomeR-dev: TFregulomeR reveals transcription factors’ context-specific features and functions

Current TFBSs in TFregulomeR compendium v2.0.0

What's new in the version v2.0.0 - 5 March 2019:

1) 865 PWMs in mouse were added (For Canada server; for Singapore server coming soon).

Previous TFregulomeR data compendium

version: 1.2.0 - 6 September 2019

What's new in the version v1.2.0 1) More detailed information about motifs added: i) consistency with the existing databases (HOCOMOCO and JASPAR); ii) correlation of the motifs identified by different motif callers, MEME-ChIP and HOMER, if not consistent or not recorded in the databases.

version: 1.1.0 - 31 July 2019

What's new in the version v1.1.0: 1) 92 TFBSs with DNA methylation levels were included from MethMotif 2) Tag fold change values were added for each TF peak set. Tag fold change values were obtained from MACS2 outputs and it measures the fold change of reads in the TF ChIP-seq compared to the control ChIP-seq 3) Re-annotate cell and tissue names.

version: 1.0.0 - 7 May 2019

| Item | Count | | :---------:|:------:| | TFBS | 1376 | | Unique TF | 374 | | TFBS with DNA methylation records | 563 | | Species | human | | Organ | stem_cell, blood_and_lymph, connective_tissue, colorectum, brain, bone, stomach, prostate, breast, pancreas, skin, kidney, lung, eye, esophagus, heart, muscle, uterus, spleen, cervix, testis, liver, adrenal_gland, neck_and_mouth, pleura, ovary, thymus, fallopian, vagina | | Sample type | primary_cells, cell_line, tissue | Cell or tissue | 423 | | Disease state | normal, tumor, Simpson_Golabi_Behmel_syndrome, progeria, metaplasia, unknown, immortalized, premetastatic| | Source | GTRD, MethMotif |

linquynus/TFregulomeR-dev documentation built on April 23, 2022, 11:11 a.m.