Within-species exploratory view · GSE43013

Spiny mouse native expression

Acomys cahirinus

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
3
Native features
8,614
Expression unit
GEO-supplied FPKM
3 samples in this species view
8,614 source-native feature IDs
GSE43013 GEO-supplied FPKM
1 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.

Spiny mouse GSE43013 PCA Scatter plot of 3 samples. Each point is keyboard focusable and labelled by accession and tissue. aca.lv.1 · Liver · PC1 -7.14 · PC2 -12.78 aca.lv.2 · Liver · PC1 -15.89 · PC2 9.91 aca.lv.3 · Liver · PC1 23.03 · PC2 2.87
Observed ranges: PC1 -15.89 to 23.03; PC2 -12.78 to 9.91.

Tissue legend

  • Liver3
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
aca.lv.1 ↗ GSM1054986 Liver 8,608 3.981e+6 20.9387
aca.lv.2 ↗ GSM1054987 Liver 8,607 4.467e+6 20.6986
aca.lv.3 ↗ GSM1054988 Liver 8,608 5.057e+6 16.9218
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
    tRNA-Leu-2
    log1p variance
    37.8284
    mean native value
    14,105.3
    detected samples
    1/3
  2. 02
    tRNA-Lys
    log1p variance
    37.1459
    mean native value
    25,635.1
    detected samples
    2/3
  3. 03
    tRNA-Arg
    log1p variance
    29.4339
    mean native value
    8,972.5
    detected samples
    2/3
  4. 04
    tRNA-Trp
    log1p variance
    28.2889
    mean native value
    3,339.6
    detected samples
    1/3
  5. 05
    tRNA-Val
    log1p variance
    27.1504
    mean native value
    2,769.2
    detected samples
    1/3
  6. 06
    ACAG00000009403
    log1p variance
    5.7649
    mean native value
    30.4280
    detected samples
    3/3
  7. 07
    ACAG00000006138
    log1p variance
    3.9199
    mean native value
    71.5039
    detected samples
    3/3
  8. 08
    ACAG00000001643
    log1p variance
    2.8782
    mean native value
    20.3011
    detected samples
    3/3
  9. 09
    ACAG00000009409
    log1p variance
    2.7181
    mean native value
    14.8219
    detected samples
    3/3
  10. 10
    ACAG00000008848
    log1p variance
    2.1972
    mean native value
    8.0136
    detected samples
    2/3
  11. 11
    ACAG00000009495
    log1p variance
    1.9803
    mean native value
    6.5073
    detected samples
    3/3
  12. 12
    ACAG00000009478
    log1p variance
    1.8561
    mean native value
    6.1782
    detected samples
    2/3
  13. 13
    ACAG00000000524
    log1p variance
    1.7330
    mean native value
    1,069.3
    detected samples
    3/3
  14. 14
    ACAG00000009368
    log1p variance
    1.6837
    mean native value
    77.0232
    detected samples
    3/3
  15. 15
    ACAG00000000099
    log1p variance
    1.4926
    mean native value
    110.5134
    detected samples
    3/3
  16. 16
    ACAG00000006516
    log1p variance
    1.3721
    mean native value
    105.6475
    detected samples
    3/3
  17. 17
    ACAG00000002737
    log1p variance
    1.3557
    mean native value
    17.0422
    detected samples
    3/3
  18. 18
    ACAG00000000485
    log1p variance
    1.3327
    mean native value
    63.8080
    detected samples
    3/3
  19. 19
    ACAG00000000438
    log1p variance
    1.3006
    mean native value
    44.7808
    detected samples
    3/3
  20. 20
    ACAG00000009313
    log1p variance
    1.2766
    mean native value
    6.4049
    detected samples
    3/3
  21. 21
    ACAG00000003401
    log1p variance
    1.2475
    mean native value
    6.3995
    detected samples
    3/3
  22. 22
    ACAG00000009373
    log1p variance
    1.2406
    mean native value
    8.7303
    detected samples
    3/3
  23. 23
    ACAG00000005612
    log1p variance
    1.2391
    mean native value
    70.3246
    detected samples
    3/3
  24. 24
    ACAG00000001043
    log1p variance
    1.1801
    mean native value
    11.3201
    detected samples
    3/3
  25. 25
    ACAG00000009410
    log1p variance
    1.1596
    mean native value
    6.8825
    detected samples
    3/3
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 →