Within-species exploratory view · GSE43013

American black bear native expression

Ursus americanus

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
6
Native features
14,452
Expression unit
GEO-supplied FPKM
6 samples in this species view
14,452 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.

American black bear GSE43013 PCA Scatter plot of 6 samples. Each point is keyboard focusable and labelled by accession and tissue. uam.lv.2 · Liver · PC1 134.72 · PC2 -34.40 uam.lv.3 · Liver · PC1 139.64 · PC2 -31.20 uam.kd.1 · Kidney · PC1 -103.44 · PC2 -75.79 uam.kd.2 · Kidney · PC1 -105.12 · PC2 -79.20 uam.br.1 · Brain · PC1 -49.21 · PC2 107.77 uam.br.2 · Brain · PC1 -16.59 · PC2 112.82
Observed ranges: PC1 -105.12 to 139.64; PC2 -79.20 to 112.82.

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
uam.lv.2 ↗ GSM1055037 Liver 12,591 4.041e+7 3.2445
uam.lv.3 ↗ GSM1055038 Liver 12,224 6.567e+7 3.2442
uam.kd.1 ↗ GSM1055082 Kidney 14,080 5.415e+7 17.7221
uam.kd.2 ↗ GSM1055083 Kidney 14,088 4.240e+7 18.4512
uam.br.1 ↗ GSM1055127 Brain 14,041 8.200e+7 15.8119
uam.br.2 ↗ GSM1055128 Brain 13,967 1.190e+8 13.0232
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
    UAMG00000000073
    log1p variance
    14.9754
    mean native value
    12,523.6
    detected samples
    6/6
  2. 02
    UAMG00000006051
    log1p variance
    14.9086
    mean native value
    1,107.2
    detected samples
    6/6
  3. 03
    UAMG00000002048
    log1p variance
    14.1090
    mean native value
    1,245.3
    detected samples
    5/6
  4. 04
    UAMG00000013932
    log1p variance
    14.0021
    mean native value
    908.8726
    detected samples
    5/6
  5. 05
    UAMG00000002006
    log1p variance
    13.9942
    mean native value
    3,511.3
    detected samples
    6/6
  6. 06
    UAMG00000000174
    log1p variance
    13.8776
    mean native value
    4,142.6
    detected samples
    6/6
  7. 07
    UAMG00000001877
    log1p variance
    13.8152
    mean native value
    46,893.0
    detected samples
    6/6
  8. 08
    UAMG00000008033
    log1p variance
    13.8098
    mean native value
    7,891.8
    detected samples
    6/6
  9. 09
    UAMG00000000162
    log1p variance
    13.7868
    mean native value
    12,336.7
    detected samples
    6/6
  10. 10
    UAMG00000001864
    log1p variance
    13.4025
    mean native value
    2,043.4
    detected samples
    6/6
  11. 11
    UAMG00000019750
    log1p variance
    13.3776
    mean native value
    2,670.5
    detected samples
    6/6
  12. 12
    UAMG00000000084
    log1p variance
    13.1760
    mean native value
    2,749.9
    detected samples
    6/6
  13. 13
    UAMG00000006273
    log1p variance
    12.9971
    mean native value
    576.3704
    detected samples
    6/6
  14. 14
    UAMG00000001783
    log1p variance
    12.8749
    mean native value
    3,268.4
    detected samples
    6/6
  15. 15
    UAMG00000008122
    log1p variance
    12.7023
    mean native value
    1,833.1
    detected samples
    6/6
  16. 16
    UAMG00000013682
    log1p variance
    12.6087
    mean native value
    2,576.2
    detected samples
    6/6
  17. 17
    UAMG00000000103
    log1p variance
    12.5504
    mean native value
    728.4774
    detected samples
    5/6
  18. 18
    UAMG00000001853
    log1p variance
    12.5314
    mean native value
    534.8240
    detected samples
    4/6
  19. 19
    UAMG00000013836
    log1p variance
    12.5010
    mean native value
    419.9511
    detected samples
    3/6
  20. 20
    UAMG00000002939
    log1p variance
    12.4968
    mean native value
    788.6986
    detected samples
    6/6
  21. 21
    UAMG00000003003
    log1p variance
    12.4136
    mean native value
    1,890.8
    detected samples
    6/6
  22. 22
    UAMG00000000024
    log1p variance
    12.3646
    mean native value
    410.1415
    detected samples
    6/6
  23. 23
    UAMG00000009140
    log1p variance
    12.1516
    mean native value
    644.7246
    detected samples
    6/6
  24. 24
    UAMG00000002432
    log1p variance
    12.0830
    mean native value
    1,171.4
    detected samples
    6/6
  25. 25
    UAMG00000001975
    log1p variance
    11.8962
    mean native value
    6,635.5
    detected samples
    6/6
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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