#ID = transcript_cluster_id
#GB_LIST = GenBank and RefSeq Accessions from mrna_assignment column
#SPOT_ID = genomic location of the transcript cluster in the version of the genome assembly used at annotation time. Coordinates are standard 1-based (length=stop-start+1).
#seqname = chromosome number
#RANGE_GB = NCBI RefSeq for chromosome of current build
#RANGE_STRAND = strand (+|-)
#RANGE_START = start (integer). Coordinates are standard 1-based (length=stop-start+1).
#RANGE_STOP = stop (integer). Coordinates are standard 1-based (length=stop-start+1).
#total_probes = Total number of probes contained by this transcript cluster.
#gene_assignment = Gene information for each assigned mRNA for mRNAs that corresponds to known genes (multipart).
#mrna_assignment = Description of the public mRNAs that should be detected by the sets within this transcript cluster based on sequence alignment (multipart).
#category = Array design category of the transcript cluster
ID GB_LIST SPOT_ID seqname RANGE_GB RANGE_STRAND RANGE_START RANGE_STOP total_probes gene_assignment mrna_assignment category
7896736 chr1:53049-54936 chr1 NC_000001.10 + 53049 54936 7 --- NONHSAT060105 // NONCODE // Non-coding transcript identified by NONCODE // chr1 // 100 // 100 // 7 // 7 // 0 main
7896738 chr1:63015-63887 chr1 NC_000001.10 + 63015 63887 31 ENST00000328113 // OR4G2P // olfactory receptor, family 4, subfamily G, member 2 pseudogene // --- // --- /// ENST00000492842 // OR4G11P // olfactory receptor, family 4, subfamily G, member 11 pseudogene // --- // --- /// ENST00000588632 // OR4G1P // olfactory receptor, family 4, subfamily G, member 1 pseudogene // --- // --- ENST00000328113 // ENSEMBL // havana:known chromosome:GRCh38:15:101926805:101927707:-1 gene:ENSG00000183909 gene_biotype:unprocessed_pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 100 // 100 // 31 // 31 // 0 /// ENST00000492842 // ENSEMBL // havana:known chromosome:GRCh38:1:62948:63887:1 gene:ENSG00000240361 gene_biotype:unprocessed_pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 100 // 100 // 31 // 31 // 0 /// ENST00000588632 // ENSEMBL // havana:known chromosome:GRCh38:19:104535:105471:1 gene:ENSG00000267310 gene_biotype:unprocessed_pseudogene transcript_biotype:unprocessed_pseudogene // chr1 // 100 // 100 // 31 // 31 // 0 /// NONHSAT000016 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100 // 31 // 31 // 0 /// NONHSAT051704 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100 // 31 // 31 // 0 /// NONHSAT060106 // NONCODE // Non-coding transcript identified by NONCODE: Linc // chr1 // 100 // 100 // 31 // 31 // 0 main
7896740 NM_001004195,NM_001005240,NM_001005484,BC136848,BC136867,BC136907,BC136908 chr1:69091-70008 chr1 NC_000001.10 + 69091 70008 24 NM_001004195 // OR4F4 // olfactory receptor, family 4, subfamily F, member 4 // 15q26.3 // 26682 /// NM_001005240 // OR4F17 // olfactory receptor, family 4, subfamily F, member 17 // 19p13.3 // 81099 /// NM_001005484 // OR4F5 // olfactory receptor, family 4, subfamily F, member 5 // 1p36.33 // 79501 /// ENST00000318050 // OR4F17 // olfactory receptor, family 4, subfamily F, member 17 // 19p13.3 // 81099 /// ENST00000326183 // OR4F4 // olfactory receptor, family 4, subfamily F, member 4 // 15q26.3 // 26682 /// ENST00000335137 // OR4F5 // olfactory receptor, family 4, subfamily F, member 5 // 1p36.33 // 79501 /// ENST00000585993 // OR4F17 // olfactory receptor, family 4, subfamily F, member 17 // 19p13.3 // 81099 /// BC136848 // OR4F17 // olfactory receptor, family 4, subfamily F, member 17 // 19p13.3 // 81099 /// BC136867 // OR4F17 // olfactory receptor, family 4, subfamily F, member 17 // 19p13.3 // 81099 /// BC136907 // OR4F4 // olfactory receptor, family 4, subfamily F, member 4 // 15q26.3 // 26682 /// BC136908 // OR4F4 // olfactory receptor, family 4, subfamily F, member 4 // 15q26.3 // 26682 NM_001004195 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 4 (OR4F4), mRNA. // chr1 // 100 // 100 // 24 // 24 // 0 /// NM_001005240 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 17 (OR4F17), mRNA. // chr1 // 100 // 100 // 24 // 24 // 0 /// NM_001005484 // RefSeq // Homo sapiens olfactory receptor, family 4, subfamily F, member 5 (OR4F5), mRNA. // chr1 // 100 // 100 // 24 // 24 // 0 /// ENST00000318050 // ENSEMBL // ensembl:known chromosome:GRCh38:19:110643:111696:1 gene:ENSG00000176695 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 24 // 24 // 0 /// ENST00000326183 // ENSEMBL // ensembl_havana_transcript:known chromosome:GRCh38:15:101922042:101923095:-1 gene:ENSG00000177693 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 24 // 24 // 0 /// ENST00000335137 // ENSEMBL // ensembl_havana_transcript:known chromosome:GRCh38:1:69091:70008:1 gene:ENSG00000186092 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 24 // 24 // 0 /// ENST00000585993 // ENSEMBL // havana:known chromosome:GRCh38:19:107461:111696:1 gene:ENSG00000176695 gene_biotype:protein_coding transcript_biotype:protein_coding // chr1 // 100 // 100 // 24 // 24 // 0 /// BC136848 // GenBank // Homo sapiens olfactory receptor, family 4, subfamily F, member 17, mRNA (cDNA clone MGC:168462 IMAGE:9020839), complete cds. // chr1 // 100 // 100 // 24 // 24 // 0 /// BC136867 // GenBank // Homo sapiens olfactory receptor, family 4, subfamily F, member 17, mRNA (cDNA clone MGC:168481 IMAGE:9020858), complete cds. // chr1 // 100 // 100 // 24 // 24 // 0 /// BC136907 // GenBank // Homo sapiens olfactory receptor, family 4, subfamily F, member 4, mRNA (cDNA clone MGC:168521 IMAGE:9020898), complete cds. // chr1 // 100 // 100 // 24 // 24 // 0 /// BC136908 // GenBank // Homo sapiens olfactory receptor, family 4, subfamily F, member 4, mRNA (cDNA clone MGC:168522 IMAGE:9020899), complete cds. // chr1 // 100 // 100 // 24 // 24 // 0 /// ENST00000618231 // ENSEMBL // havana:known chromosome:GRCh38:19:110613:111417:1 gene:ENSG00000176695 gene_biotype:protein_coding transcript_biotype:retained_intron // chr1 // 100 // 88 // 21 // 21 // 0 main
7896742 NR_024437,XM_006711854,XM_006726377,XR_430662,AK298283,AL137655,BC032332,BC118988,BC122537,BC131690,NM_207366,AK301928,BC071667 chr1:334129-334296 chr1 NC_000001.10 + 334129 334296 6 NR_024437 // LOC728323 // uncharacterized LOC728323 // 2q37.3 // 728323 /// XM_006711854 // LOC101060626 // F-box only protein 25-like // --- // 101060626 /// XM_006726377 // LOC101060626 // F-box only protein 25-like // --- // 101060626 /// XR_430662 // LOC101927097 // uncharacterized LOC101927097 // --- // 101927097 /// ENST00000279067 // LINC00266-1 // long intergenic non-protein coding RNA 266-1 // 20q13.33 // 140849 /// ENST00000431812 // LOC101928706 // uncharacterized LOC101928706 // --- // 101928706 /// ENST00000431812 // LOC101929823 // uncharacterized LOC101929823 // --- // 101929823 /// ENST00000433444 // LOC728323 // uncharacterized LOC728323 // 2q37.3 // 728323 /// ENST00000436899 // LINC00266-3 // long intergenic non-protein coding RNA 266-3 // --- // --- /// ENST00000445252 // LINC00266-1 // long intergenic non-protein coding RNA 266-1 // 20q13.33 // 140849 /// ENST00000455207 // LOC101928706 // uncharacterized LOC101928706 // --- // 101928706 /// ENST00000455207 // LOC101929823 // uncharacterized LOC101929823 // --- // 101929823 /// ENST00000455464 // LOC101928706 // uncharacterized LOC101928706 // --- // 101928706 /// ENST00000455464 // LOC101929823 // uncharacterized LOC101929823 // --- // 101929823 /// ENST00000456398 // LOC728323 // uncharacterized LOC728323 // 2q37.3 // 728323 /// ENST00000601814 // LOC101928706 // uncharacterized LOC101928706 // --- // 101928706 /// ENST00000601814 // LOC101929823 // uncharacterized LOC101929823 // --- // 101929823 /// AK298283 // LOC728323 // uncharacterized LOC728323 // 2q37.3 // 728323 /// AL137
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基于生物信息学及机器学习预测与 NAT10 相关的下游基.zip (55个子文件)
NAT10-master
combine.py 860B
plot
plotNetwork.py 2KB
plotHeapMap.py 1KB
plotPCAFigure.py 1KB
mergeMLResults.py 1KB
PCA.py 1005B
datasets
processed
GSE206917.csv 1.56MB
overall.csv 1.56MB
GSE207002.csv 3.06MB
GSE82139.csv 2.68MB
raw
GSE207002
GSM6267794_Con2_3.txt 324KB
GSM6267801_RR2_1.txt 330KB
GSM6267793_Con2_2.txt 325KB
GSM6267800_RR1_3.txt 327KB
GSM6267805_RR3_2.txt 327KB
GSM6267804_RR3_1.txt 327KB
GSM6267791_Con1_3.txt 306KB
GSM6267796_Con3_2.txt 322KB
GSM6267789_Con1_1.txt 306KB
GSM6267790_Con1_2.txt 307KB
GSM6267799_RR1_2.txt 327KB
GSM6267792_Con2_1.txt 324KB
GSM6267806_RR3_3.txt 327KB
GSM6267795_Con3_1.txt 322KB
GSM6267798_RR1_1.txt 327KB
GSM6267803_RR2_3.txt 329KB
GSM6267802_RR2_2.txt 330KB
GSM6267797_Con3_3.txt 321KB
GSE82139
GSE82139.csv 3.15MB
GPL6244-17930.txt 94.75MB
GSE82139_series_matrix.txt 5.56MB
GSE206917
GSE206917_tissue_gene_expression.xls 3.41MB
GSE206917_U251_gene_expression.xls 4.27MB
GSE206917_U87_gene_expression.xls 4.23MB
randomForest.py 1KB
SVM.py 1KB
datasetsProcess
extractGSE206917Data.py 3KB
mergeDatasets.py 1KB
changeGSE82139.py 824B
mergeGSE207002Data.py 1KB
GSE82139_series_matrix.txt 5.56MB
convertGSE82139.R 2KB
result
svm_feature_importances.csv 414KB
pca_with_NAT10.png 42KB
pca_loadings.csv 404KB
heatmap_with_NAT10.png 153KB
NAT10_high_correlation_genes.csv 63KB
gene_interaction_network_based_on_scores.png 1.34MB
selected_genes_common_to_both_criteria.csv 3KB
combined_gene_scores.csv 390KB
significant_genes_from_limma.csv 13KB
all.limmaOut.csv 1.71MB
top_genes_in_selected_criteria.csv 1KB
feature_importances.csv 184KB
DEA.R 5KB
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