Within-species exploratory view · GSE43013

Domestic cattle native expression

Bos taurus

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
24,616
Expression unit
GEO-supplied FPKM
6 samples in this species view
24,616 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 cattle GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. bta.lv.1 · Liver · PC1 -103.69 · PC2 -56.36 bta.lv.2 · Liver · PC1 -97.95 · PC2 -47.94 bta.kd.1 · Kidney · PC1 -15.37 · PC2 85.44 bta.kd.2 · Kidney · PC1 -8.38 · PC2 93.86 bta.br.1 · Brain · PC1 109.96 · PC2 -39.55 bta.br.2 · Brain · PC1 115.42 · PC2 -35.45
Observed ranges: PC1 -103.69 to 115.42; PC2 -56.36 to 93.86.

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
bta.lv.1 ↗ GSM1054989 Liver 15,208 932,262.0 4.0908
bta.lv.2 ↗ GSM1054990 Liver 15,511 1.077e+6 5.1548
bta.kd.1 ↗ GSM1055039 Kidney 16,766 3.611e+6 8.7560
bta.kd.2 ↗ GSM1055040 Kidney 17,289 3.944e+6 9.4827
bta.br.1 ↗ GSM1055084 Brain 17,267 1.488e+6 9.0625
bta.br.2 ↗ GSM1055085 Brain 16,968 3.261e+6 10.0620
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
    ENSBTAG00000040302
    log1p variance
    34.4661
    mean native value
    28,973.3
    detected samples
    2/6
  2. 02
    ENSBTAG00000043551
    log1p variance
    30.1163
    mean native value
    11,995.1
    detected samples
    3/6
  3. 03
    ENSBTAG00000043549
    log1p variance
    27.5755
    mean native value
    21,580.4
    detected samples
    4/6
  4. 04
    ENSBTAG00000043576
    log1p variance
    26.8696
    mean native value
    6,465.9
    detected samples
    3/6
  5. 05
    ENSBTAG00000043555
    log1p variance
    26.3143
    mean native value
    8,803.2
    detected samples
    3/6
  6. 06
    ENSBTAG00000043552
    log1p variance
    25.9086
    mean native value
    6,253.0
    detected samples
    3/6
  7. 07
    ENSBTAG00000001638
    log1p variance
    25.8340
    mean native value
    10,135.4
    detected samples
    4/6
  8. 08
    ENSBTAG00000037500
    log1p variance
    25.7812
    mean native value
    6,211.8
    detected samples
    2/6
  9. 09
    ENSBTAG00000043565
    log1p variance
    25.5230
    mean native value
    7,158.1
    detected samples
    2/6
  10. 10
    ENSBTAG00000006745
    log1p variance
    24.7669
    mean native value
    11,598.3
    detected samples
    6/6
  11. 11
    ENSBTAG00000043557
    log1p variance
    24.2146
    mean native value
    4,586.4
    detected samples
    2/6
  12. 12
    ENSBTAG00000022120
    log1p variance
    24.1027
    mean native value
    8,304.9
    detected samples
    6/6
  13. 13
    ENSBTAG00000043573
    log1p variance
    23.8197
    mean native value
    4,123.0
    detected samples
    3/6
  14. 14
    ENSBTAG00000045613
    log1p variance
    22.6877
    mean native value
    6,360.2
    detected samples
    3/6
  15. 15
    ENSBTAG00000003564
    log1p variance
    22.4766
    mean native value
    3,894.8
    detected samples
    4/6
  16. 16
    ENSBTAG00000042368
    log1p variance
    22.1499
    mean native value
    3,039.9
    detected samples
    2/6
  17. 17
    ENSBTAG00000042758
    log1p variance
    21.7502
    mean native value
    2,614.0
    detected samples
    3/6
  18. 18
    ENSBTAG00000043572
    log1p variance
    21.5488
    mean native value
    2,824.1
    detected samples
    2/6
  19. 19
    ENSBTAG00000046540
    log1p variance
    21.4864
    mean native value
    3,262.1
    detected samples
    4/6
  20. 20
    ENSBTAG00000006354
    log1p variance
    21.1676
    mean native value
    13,093.3
    detected samples
    6/6
  21. 21
    ENSBTAG00000022395
    log1p variance
    21.1088
    mean native value
    4,472.4
    detected samples
    4/6
  22. 22
    ENSBTAG00000043548
    log1p variance
    20.8203
    mean native value
    2,293.2
    detected samples
    2/6
  23. 23
    ENSBTAG00000043544
    log1p variance
    20.6081
    mean native value
    2,239.7
    detected samples
    2/6
  24. 24
    ENSBTAG00000043566
    log1p variance
    20.3397
    mean native value
    4,295.4
    detected samples
    4/6
  25. 25
    ENSBTAG00000047040
    log1p variance
    20.2549
    mean native value
    2,162.4
    detected samples
    4/6
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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