Within-species exploratory view · GSE43013

House mouse native expression

Mus musculus

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
9
Native features
37,511
Expression unit
GEO-supplied FPKM
9 samples in this species view
37,511 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.

House mouse GSE43013 PCA Scatter plot of 9 samples. Each point is keyboard focusable and labelled by accession and tissue. mus.lv.1 · Liver · PC1 -94.82 · PC2 -59.59 mus.lv.2 · Liver · PC1 -94.35 · PC2 -62.19 mus.lv.3 · Liver · PC1 -92.91 · PC2 -58.12 mus.kd.1 · Kidney · PC1 -37.45 · PC2 79.37 mus.kd.2 · Kidney · PC1 -30.86 · PC2 85.41 mus.kd.3 · Kidney · PC1 -28.88 · PC2 85.13 mus.br.1 · Brain · PC1 126.04 · PC2 -23.79 mus.br.2 · Brain · PC1 125.19 · PC2 -22.43 mus.br.3 · Brain · PC1 128.04 · PC2 -23.79
Observed ranges: PC1 -94.82 to 128.04; PC2 -62.19 to 85.41.

Tissue legend

  • Brain3
  • Kidney3
  • 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
mus.lv.1 ↗ GSM1055018 Liver 18,522 8.276e+6 3.1159
mus.lv.2 ↗ GSM1055019 Liver 19,262 8.007e+6 2.8816
mus.lv.3 ↗ GSM1055020 Liver 19,214 8.548e+6 2.9538
mus.kd.1 ↗ GSM1055066 Kidney 20,493 6.743e+6 3.9528
mus.kd.2 ↗ GSM1055067 Kidney 20,639 2.492e+6 4.4084
mus.kd.3 ↗ GSM1055068 Kidney 20,621 2.342e+6 4.5834
mus.br.1 ↗ GSM1055111 Brain 22,103 4.825e+6 4.6719
mus.br.2 ↗ GSM1055112 Brain 22,215 5.470e+6 4.8099
mus.br.3 ↗ GSM1055113 Brain 22,440 5.013e+6 4.5347
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
    ENSMUSG00000084559
    log1p variance
    27.1903
    mean native value
    11,622.0
    detected samples
    3/9
  2. 02
    ENSMUSG00000076258
    log1p variance
    27.0186
    mean native value
    23,702.0
    detected samples
    6/9
  3. 03
    ENSMUSG00000064365
    log1p variance
    23.7623
    mean native value
    6,144.7
    detected samples
    3/9
  4. 04
    ENSMUSG00000093285
    log1p variance
    21.4732
    mean native value
    4,311.0
    detected samples
    5/9
  5. 05
    ENSMUSG00000064361
    log1p variance
    20.8811
    mean native value
    3,411.3
    detected samples
    5/9
  6. 06
    ENSMUSG00000064366
    log1p variance
    20.6498
    mean native value
    3,323.2
    detected samples
    5/9
  7. 07
    ENSMUSG00000064364
    log1p variance
    20.3133
    mean native value
    2,960.2
    detected samples
    5/9
  8. 08
    ENSMUSG00000093076
    log1p variance
    19.8888
    mean native value
    2,673.5
    detected samples
    5/9
  9. 09
    ENSMUSG00000064359
    log1p variance
    19.6453
    mean native value
    2,519.1
    detected samples
    3/9
  10. 10
    ENSMUSG00000079600
    log1p variance
    19.4705
    mean native value
    2,626.2
    detected samples
    5/9
  11. 11
    ENSMUSG00000064344
    log1p variance
    19.1677
    mean native value
    17,498.9
    detected samples
    7/9
  12. 12
    ENSMUSG00000093231
    log1p variance
    18.9402
    mean native value
    4,849.3
    detected samples
    6/9
  13. 13
    ENSMUSG00000092772
    log1p variance
    18.6161
    mean native value
    1,675.3
    detected samples
    4/9
  14. 14
    ENSMUSG00000064355
    log1p variance
    18.5283
    mean native value
    1,834.8
    detected samples
    3/9
  15. 15
    ENSMUSG00000093264
    log1p variance
    18.0864
    mean native value
    3,911.4
    detected samples
    7/9
  16. 16
    ENSMUSG00000078674
    log1p variance
    17.8357
    mean native value
    4,144.7
    detected samples
    7/9
  17. 17
    ENSMUSG00000032758
    log1p variance
    17.3947
    mean native value
    7,214.4
    detected samples
    9/9
  18. 18
    ENSMUSG00000092696
    log1p variance
    17.2498
    mean native value
    1,206.0
    detected samples
    4/9
  19. 19
    ENSMUSG00000078686
    log1p variance
    17.0599
    mean native value
    3,897.0
    detected samples
    8/9
  20. 20
    ENSMUSG00000073842
    log1p variance
    16.7009
    mean native value
    2,817.6
    detected samples
    8/9
  21. 21
    ENSMUSG00000069885
    log1p variance
    15.9903
    mean native value
    997.8422
    detected samples
    3/9
  22. 22
    ENSMUSG00000066154
    log1p variance
    15.8087
    mean native value
    1,802.3
    detected samples
    7/9
  23. 23
    ENSMUSG00000077868
    log1p variance
    15.7618
    mean native value
    2,106.3
    detected samples
    6/9
  24. 24
    ENSMUSG00000092748
    log1p variance
    15.6974
    mean native value
    1,012.7
    detected samples
    4/9
  25. 25
    ENSMUSG00000078672
    log1p variance
    15.6749
    mean native value
    2,091.9
    detected samples
    9/9
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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