Within-species exploratory view · GSE43013

Domestic pig native expression

Sus scrofa

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
20,460
Expression unit
GEO-supplied FPKM
6 samples in this species view
20,460 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 pig GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. ssc.lv.1 · Liver · PC1 -86.93 · PC2 -65.87 ssc.lv.2 · Liver · PC1 -86.78 · PC2 -65.90 ssc.kd.1 · Kidney · PC1 -40.08 · PC2 84.93 ssc.kd.2 · Kidney · PC1 -39.15 · PC2 84.40 ssc.br.1 · Brain · PC1 121.56 · PC2 -20.24 ssc.br.2 · Brain · PC1 131.38 · PC2 -17.33
Observed ranges: PC1 -86.93 to 131.38; PC2 -65.90 to 84.93.

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
ssc.lv.1 ↗ GSM1055031 Liver 13,103 2.711e+6 5.4887
ssc.lv.2 ↗ GSM1055032 Liver 12,987 2.590e+6 6.0262
ssc.kd.1 ↗ GSM1055078 Kidney 13,724 8.937e+6 8.8802
ssc.kd.2 ↗ GSM1055079 Kidney 13,938 1.166e+7 8.7250
ssc.br.1 ↗ GSM1055123 Brain 14,532 4.859e+6 12.9011
ssc.br.2 ↗ GSM1055124 Brain 15,002 1.454e+7 12.4493
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
    ENSSSCG00000008798
    log1p variance
    41.0908
    mean native value
    105,208.8
    detected samples
    3/6
  2. 02
    ENSSSCG00000015745
    log1p variance
    32.8503
    mean native value
    24,905.9
    detected samples
    3/6
  3. 03
    ENSSSCG00000018073
    log1p variance
    31.3614
    mean native value
    17,445.7
    detected samples
    3/6
  4. 04
    ENSSSCG00000018071
    log1p variance
    28.3214
    mean native value
    10,579.2
    detected samples
    3/6
  5. 05
    ENSSSCG00000003122
    log1p variance
    27.3953
    mean native value
    31,655.3
    detected samples
    4/6
  6. 06
    ENSSSCG00000009204
    log1p variance
    27.3666
    mean native value
    8,463.2
    detected samples
    2/6
  7. 07
    ENSSSCG00000018074
    log1p variance
    27.0568
    mean native value
    9,319.4
    detected samples
    3/6
  8. 08
    ENSSSCG00000018072
    log1p variance
    25.1969
    mean native value
    11,841.1
    detected samples
    4/6
  9. 09
    ENSSSCG00000005827
    log1p variance
    25.1686
    mean native value
    6,462.3
    detected samples
    2/6
  10. 10
    ENSSSCG00000018088
    log1p variance
    24.9464
    mean native value
    5,376.8
    detected samples
    2/6
  11. 11
    ENSSSCG00000018077
    log1p variance
    23.3136
    mean native value
    3,448.2
    detected samples
    3/6
  12. 12
    ENSSSCG00000018090
    log1p variance
    22.2562
    mean native value
    3,167.1
    detected samples
    2/6
  13. 13
    ENSSSCG00000018062
    log1p variance
    21.6808
    mean native value
    2,774.6
    detected samples
    2/6
  14. 14
    ENSSSCG00000018085
    log1p variance
    21.6707
    mean native value
    5,948.7
    detected samples
    4/6
  15. 15
    ENSSSCG00000008948
    log1p variance
    21.6598
    mean native value
    35,544.6
    detected samples
    6/6
  16. 16
    ENSSSCG00000005258
    log1p variance
    21.5508
    mean native value
    2,674.1
    detected samples
    2/6
  17. 17
    ENSSSCG00000020136
    log1p variance
    21.4006
    mean native value
    2,386.2
    detected samples
    3/6
  18. 18
    ENSSSCG00000018083
    log1p variance
    21.1926
    mean native value
    2,504.0
    detected samples
    2/6
  19. 19
    ENSSSCG00000019653
    log1p variance
    21.0095
    mean native value
    4,927.1
    detected samples
    4/6
  20. 20
    ENSSSCG00000011571
    log1p variance
    20.9727
    mean native value
    3,106.0
    detected samples
    3/6
  21. 21
    ENSSSCG00000018068
    log1p variance
    20.7318
    mean native value
    86,950.6
    detected samples
    5/6
  22. 22
    ENSSSCG00000019025
    log1p variance
    20.0544
    mean native value
    5,191.0
    detected samples
    4/6
  23. 23
    ENSSSCG00000020418
    log1p variance
    19.8311
    mean native value
    3,955.8
    detected samples
    4/6
  24. 24
    ENSSSCG00000002484
    log1p variance
    19.8140
    mean native value
    2,338.4
    detected samples
    4/6
  25. 25
    ENSSSCG00000018174
    log1p variance
    19.4937
    mean native value
    1,747.0
    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

Back to source records → All 41 mammals →