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Oct4ESC_ChIPgenes

Predicted Oct4 bound genes in embryonic stem cells (ESC) obtained from analyzing ChIP-seq data

Bundled with ChIPXpress · exported, loads via data()

Class
data.frame
Dimensions
5,158 × 21
Missing
0
Format
rda · xz
version 2 · 196 KB
File
data/Oct4ESC_ChIPgenes.rda
Fingerprint
e254c0ca
Format documented
Yes
Source
www.ncbi.nlm.nih.gov/geo/
About this object
A table with named columnsA bordered table: a header band ruled off from the body with an empty slot over each column where its name goes, and rows of cells under it that share every edge. Nothing is in any of them.

Equal-length columns presented as a table, R's standard rectangular format. R object catalogue

Declared attributes
Row names
Yes
Columns
Column
Type
Distinct
Missing
Summary
Rank
integer
5,158
0
2 – 26329mean 1.249e+4
Min.
2
1st Qu.
5566.25
Median
12132
Mean
12493.1
3rd Qu.
19342.5
Max.
26329
Std. dev
7771.65
Skewness
0.1024
Kurtosis
-1.252
Order
ascending
Chr
character
21
0
4 – 5 characters
Start
integer
5,156
0
222285 – 196442155mean 7.685e+7
Min.
222285
1st Qu.
3.7165e+7
Median
7.48034e+7
Mean
7.68477e+7
3rd Qu.
1.12472e+8
Max.
196442155
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
End
integer
5,154
0
222599 – 196442854mean 7.685e+7
Min.
222599
1st Qu.
3.71657e+7
Median
7.48039e+7
Mean
7.68483e+7
3rd Qu.
1.12473e+8
Max.
196442854
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
Strand
character
1
0
1 characters
Annotation
character
5,158
0
1 – 18 characters
Gene
character
5,158
0
9 – 12 characters
EntrezID
integer
5,158
0
11298 – 100504663mean 2.858e+5
Min.
11298
1st Qu.
20333.5
Median
68755.5
Mean
285848
3rd Qu.
212642
Max.
100504663
Std. dev
4.17493e+6
Skewness
23.84
Kurtosis
567
Outliers
730 low · 73 high
peak_length
integer
54
0
105 – 3115mean 569.3
Min.
105
1st Qu.
420
Median
560
Mean
569.33
3rd Qu.
700
Max.
3115
Std. dev
232.312
Skewness
1.586
Kurtosis
8.496
Outliers
1130 low · 113 high
FDR
numeric
395
0
0 – 0.0988mean 0.0089
Min.
0
1st Qu.
0.0003
Median
0.0003
Mean
0.0089
3rd Qu.
0.0057
Max.
0.0988
Std. dev
0.0188
Skewness
2.707
Kurtosis
6.984
Zeros
421
Outliers
9540 low · 954 high
Order
ascending
left_peakboundary
integer
5,158
0
222322 – 196442462mean 7.685e+7
Min.
222322
1st Qu.
3.71653e+7
Median
74803602
Mean
7.68479e+7
3rd Qu.
1.12472e+8
Max.
196442462
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
right_peakboundary
integer
5,158
0
222317 – 196442542mean 7.685e+7
Min.
222317
1st Qu.
3.71653e+7
Median
7.48037e+7
Mean
7.6848e+7
3rd Qu.
1.12472e+8
Max.
196442542
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
peak_summit
integer
5,157
0
222397 – 196442492mean 7.685e+7
Min.
222397
1st Qu.
3.71654e+7
Median
7.48037e+7
Mean
7.6848e+7
3rd Qu.
1.12472e+8
Max.
196442492
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
bound_center
integer
5,158
0
222319 – 196442502mean 7.685e+7
Min.
222319
1st Qu.
3.71653e+7
Median
7.48037e+7
Mean
7.6848e+7
3rd Qu.
1.12472e+8
Max.
196442502
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
bound_width
integer
168
0
-689 – 911mean 87.25
Min.
-689
1st Qu.
51
Median
91
Mean
87.2466
3rd Qu.
126
Max.
911
Std. dev
90.4553
Skewness
-0.2586
Kurtosis
12.99
Outliers
355192 low · 163 high
maxT
numeric
4,208
0
3.1641 – 11.0453mean 4.849
Min.
3.1641
1st Qu.
3.8218
Median
4.5109
Mean
4.8487
3rd Qu.
5.5954
Max.
11.0453
Std. dev
1.2993
Skewness
1.021
Kurtosis
0.6274
Outliers
850 low · 85 high
Order
descending
maxT_pos
integer
5,155
0
222302 – 196442522mean 7.685e+7
Min.
222302
1st Qu.
37165397
Median
74803697
Mean
7.6848e+7
3rd Qu.
1.12472e+8
Max.
196442522
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
max_log2FC
numeric
4,205
0
2.06 – 7.3483mean 3.19
Min.
2.06
1st Qu.
2.5014
Median
2.9638
Mean
3.1904
3rd Qu.
3.6914
Max.
7.3483
Std. dev
0.8718
Skewness
1.021
Kurtosis
0.6274
Outliers
850 low · 85 high
Order
descending
maxFC_pos
integer
5,155
0
222302 – 196442522mean 7.685e+7
Min.
222302
1st Qu.
37165397
Median
74803697
Mean
7.6848e+7
3rd Qu.
1.12472e+8
Max.
196442522
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
minuslog10_minPoisP
numeric
2,611
0
5.0035 – 100mean 26.09
Min.
5.0035
1st Qu.
8.2388
Median
14.2238
Mean
26.0925
3rd Qu.
31.25
Max.
100
Std. dev
27.0668
Skewness
1.669
Kurtosis
1.664
Outliers
5970 low · 597 high
minPoisP_pos
integer
5,154
0
222407 – 196442487mean 7.685e+7
Min.
222407
1st Qu.
3.71654e+7
Median
7.48037e+7
Mean
7.6848e+7
3rd Qu.
1.12472e+8
Max.
196442487
Std. dev
4.49486e+7
Skewness
0.2491
Kurtosis
-0.8708
Version history
VersionReleasedSizeChangeStored asConfidence
3.232026-04-285,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.222025-10-295,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.212025-04-155,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.202024-10-295,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.192024-04-305,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.182023-10-245,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.172023-04-255,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.162022-11-015,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.152022-04-265,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.142021-10-265,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.132021-05-195,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.122020-10-275,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.112020-04-275,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.102019-10-295,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.92019-05-025,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.82018-10-305,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.72018-04-305,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.62018-01-055,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.52017-04-245,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.42016-10-175,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.32016-05-035,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.22015-10-135,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.12015-04-165,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
3.02014-10-135,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
2.142014-04-115,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
2.132013-10-145,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
2.122013-04-035,158 × 21Unchangedrda · xz
version 2 · 196 KB
exact
2.112012-10-015,158 × 21–rda · xz
version 2 · 196 KB
exact

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