Within-species exploratory view · GSE43013

Domestic dog native expression

Canis familiaris

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 → LACA content → Open GEO ↗
Samples
6
Native features
24,660
Expression unit
GEO-supplied FPKM
6 samples in this species view
24,660 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.

Domestic dog GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. caf.lv.1 · Liver · PC1 92.46 · PC2 -67.02 caf.lv.2 · Liver · PC1 91.60 · PC2 -67.80 caf.kd.1 · Kidney · PC1 41.07 · PC2 86.64 caf.kd.2 · Kidney · PC1 40.80 · PC2 87.79 caf.br.1 · Brain · PC1 -132.70 · PC2 -20.01 caf.br.2 · Brain · PC1 -133.22 · PC2 -19.60
Observed ranges: PC1 -133.22 to 92.46; PC2 -67.80 to 87.79.

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
caf.lv.1 ↗ GSM1054992 Liver 15,608 2.371e+6 5.6919
caf.lv.2 ↗ GSM1054993 Liver 15,943 3.545e+6 5.1658
caf.kd.1 ↗ GSM1055042 Kidney 17,003 7.350e+6 8.5532
caf.kd.2 ↗ GSM1055043 Kidney 16,533 9.755e+6 8.9484
caf.br.1 ↗ GSM1055087 Brain 17,264 2.965e+6 13.4369
caf.br.2 ↗ GSM1055088 Brain 17,282 2.894e+6 12.8962
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
    ENSCAFG00000022722
    log1p variance
    27.7661
    mean native value
    20,060.2
    detected samples
    4/6
  2. 02
    ENSCAFG00000022731
    log1p variance
    27.6471
    mean native value
    8,291.9
    detected samples
    3/6
  3. 03
    ENSCAFG00000022714
    log1p variance
    26.9617
    mean native value
    8,663.1
    detected samples
    2/6
  4. 04
    ENSCAFG00000003016
    log1p variance
    26.3790
    mean native value
    30,884.3
    detected samples
    6/6
  5. 05
    ENSCAFG00000025841
    log1p variance
    24.3593
    mean native value
    4,171.8
    detected samples
    3/6
  6. 06
    ENSCAFG00000022712
    log1p variance
    23.8363
    mean native value
    4,376.6
    detected samples
    3/6
  7. 07
    ENSCAFG00000028034
    log1p variance
    22.7690
    mean native value
    3,442.3
    detected samples
    2/6
  8. 08
    ENSCAFG00000022738
    log1p variance
    22.5964
    mean native value
    2,954.7
    detected samples
    3/6
  9. 09
    ENSCAFG00000026710
    log1p variance
    21.8189
    mean native value
    2,831.3
    detected samples
    2/6
  10. 10
    ENSCAFG00000022715
    log1p variance
    21.7861
    mean native value
    7,611.2
    detected samples
    4/6
  11. 11
    ENSCAFG00000020220
    log1p variance
    21.5535
    mean native value
    6,607.8
    detected samples
    5/6
  12. 12
    ENSCAFG00000013318
    log1p variance
    21.0823
    mean native value
    3,773.5
    detected samples
    4/6
  13. 13
    ENSCAFG00000026824
    log1p variance
    21.0339
    mean native value
    2,361.9
    detected samples
    3/6
  14. 14
    ENSCAFG00000026246
    log1p variance
    20.9685
    mean native value
    2,400.9
    detected samples
    2/6
  15. 15
    ENSCAFG00000002598
    log1p variance
    20.8319
    mean native value
    6,290.2
    detected samples
    5/6
  16. 16
    ENSCAFG00000022733
    log1p variance
    20.3127
    mean native value
    4,139.8
    detected samples
    4/6
  17. 17
    ENSCAFG00000022725
    log1p variance
    20.2993
    mean native value
    4,171.1
    detected samples
    4/6
  18. 18
    ENSCAFG00000022406
    log1p variance
    19.8771
    mean native value
    1,872.6
    detected samples
    3/6
  19. 19
    ENSCAFG00000026505
    log1p variance
    19.4569
    mean native value
    1,716.9
    detected samples
    2/6
  20. 20
    ENSCAFG00000022716
    log1p variance
    19.3576
    mean native value
    43,572.2
    detected samples
    5/6
  21. 21
    ENSCAFG00000022718
    log1p variance
    18.9524
    mean native value
    7,128.9
    detected samples
    1/6
  22. 22
    ENSCAFG00000024109
    log1p variance
    18.5968
    mean native value
    1,718.5
    detected samples
    3/6
  23. 23
    ENSCAFG00000017646
    log1p variance
    18.4452
    mean native value
    5,072.7
    detected samples
    6/6
  24. 24
    ENSCAFG00000027561
    log1p variance
    18.2793
    mean native value
    1,325.7
    detected samples
    2/6
  25. 25
    ENSCAFG00000025798
    log1p variance
    18.0307
    mean native value
    1,241.4
    detected samples
    2/6
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

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