Within-species exploratory view · GSE43013

White-footed mouse native expression

Peromyscus leucopus

Sample QC, log-transformed PCA, and the most variable source-native feature IDs from Per-sample GEO-supplied FPKM files.

View PCA → Open Igf1 gene profile → Source samples → Open GEO ↗
Samples
6
Native features
17,127
Expression unit
GEO-supplied FPKM
6 samples in this species view
17,127 source-native feature IDs
GSE43013 GEO-supplied FPKM
3 Table S1 tissues represented
Exploratory ordination

PCA of log1p native expression

SVD PCA after feature-wise centering after log1p(GEO-supplied FPKM). Axes apply only to this species and dataset.

White-footed mouse GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. ple.lv.1 · Liver · PC1 109.22 · PC2 -58.16 ple.lv.2 · Liver · PC1 122.91 · PC2 -67.98 ple.kd.1 · Kidney · PC1 25.76 · PC2 94.30 ple.kd.2 · Kidney · PC1 34.33 · PC2 93.82 ple.br.1 · Brain · PC1 -144.83 · PC2 -30.51 ple.br.2 · Brain · PC1 -147.39 · PC2 -31.47
Observed ranges: PC1 -147.39 to 122.91; PC2 -67.98 to 94.30.

Tissue legend

  • Brain2
  • Kidney2
  • Liver2
Transform
log1p(GEO-supplied FPKM)
Feature policy
Intersection of native feature IDs across samples within each species.
Normalization
The source reports Cufflinks FPKM; LACA applies log1p only for within-species PCA/QC.
Sample-level quality context

Detected features and expression totals

These are descriptive summaries of the supplied GEO-supplied FPKM values—not read-depth QC metrics and not thresholds for sample exclusion.

Sample Tissue Detected native features Total GEO-supplied FPKM Median positive value
ple.lv.1 ↗ GSM1055023 Liver 14,667 967,563.5 7.9780
ple.lv.2 ↗ GSM1055024 Liver 14,295 1.188e+6 5.8799
ple.kd.1 ↗ GSM1055073 Kidney 16,109 1.072e+6 16.7813
ple.kd.2 ↗ GSM1055074 Kidney 15,890 1.053e+6 15.1989
ple.br.1 ↗ GSM1055118 Brain 16,630 916,846.1 18.2290
ple.br.2 ↗ GSM1055119 Brain 16,643 887,084.0 18.7790
Source-native feature ranking

Top variable native feature IDs

Ranked by variance after log1p transformation within this exact view. IDs are reported verbatim from the source matrix and must not be treated as cross-species orthologs.

  1. 01
    PLEG00000014792
    log1p variance
    25.6034
    mean native value
    37,699.7
    detected samples
    6/6
  2. 02
    PLEG00000013970
    log1p variance
    21.7697
    mean native value
    11,338.4
    detected samples
    4/6
  3. 03
    PLEG00000016136
    log1p variance
    20.1507
    mean native value
    4,468.3
    detected samples
    6/6
  4. 04
    PLEG00000013465
    log1p variance
    19.6458
    mean native value
    2,714.8
    detected samples
    5/6
  5. 05
    PLEG00000015420
    log1p variance
    18.4753
    mean native value
    2,922.3
    detected samples
    5/6
  6. 06
    PLEG00000025023
    log1p variance
    17.9013
    mean native value
    2,852.4
    detected samples
    4/6
  7. 07
    PLEG00000016656
    log1p variance
    17.7265
    mean native value
    3,028.4
    detected samples
    4/6
  8. 08
    PLEG00000000927
    log1p variance
    16.6265
    mean native value
    5,378.3
    detected samples
    6/6
  9. 09
    PLEG00000013479
    log1p variance
    16.5358
    mean native value
    1,102.1
    detected samples
    3/6
  10. 10
    PLEG00000025195
    log1p variance
    16.4369
    mean native value
    1,618.6
    detected samples
    4/6
  11. 11
    PLEG00000014447
    log1p variance
    16.3852
    mean native value
    1,723.0
    detected samples
    6/6
  12. 12
    PLEG00000013788
    log1p variance
    16.3294
    mean native value
    1,046.1
    detected samples
    4/6
  13. 13
    PLEG00000015510
    log1p variance
    15.2002
    mean native value
    2,190.5
    detected samples
    4/6
  14. 14
    PLEG00000015457
    log1p variance
    15.0963
    mean native value
    1,305.3
    detected samples
    5/6
  15. 15
    PLEG00000013440
    log1p variance
    14.9176
    mean native value
    967.3352
    detected samples
    6/6
  16. 16
    PLEG00000016300
    log1p variance
    14.8444
    mean native value
    2,136.7
    detected samples
    6/6
  17. 17
    PLEG00000024376
    log1p variance
    14.6484
    mean native value
    5,190.4
    detected samples
    6/6
  18. 18
    PLEG00000025208
    log1p variance
    14.6104
    mean native value
    826.5395
    detected samples
    6/6
  19. 19
    PLEG00000016663
    log1p variance
    14.5369
    mean native value
    1,355.1
    detected samples
    5/6
  20. 20
    PLEG00000014664
    log1p variance
    14.0610
    mean native value
    1,571.7
    detected samples
    6/6
  21. 21
    PLEG00000016114
    log1p variance
    14.0153
    mean native value
    994.3950
    detected samples
    6/6
  22. 22
    PLEG00000016129
    log1p variance
    14.0027
    mean native value
    1,106.9
    detected samples
    5/6
  23. 23
    PLEG00000015439
    log1p variance
    13.9734
    mean native value
    1,209.8
    detected samples
    5/6
  24. 24
    PLEG00000015434
    log1p variance
    13.7965
    mean native value
    972.0879
    detected samples
    6/6
  25. 25
    PLEG00000000015
    log1p variance
    13.7657
    mean native value
    526.6360
    detected samples
    6/6
Reproducible boundary

What this page computes—and what it does not

Input

Per-sample GEO-supplied FPKM files

The source reports Cufflinks FPKM; LACA applies log1p only for within-species PCA/QC.

Within-species computation

QC · PCA · variable features

Intersection of native feature IDs across samples within each species.

Not computed

No cross-species expression test

No matrix merge, differential-expression result, lifespan regression, or causal claim is presented here.

Source integrity

GSE43013_RAW.tar

SHA-256 550e7fd866249caa7d43d85beef62dd19f4d139cc41dae0b2d0a012ccb9e3bf1

Back to source records → All 41 mammals →