Within-species exploratory view · GSE43013

Vervet native expression

Chlorocebus aethiops

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
3
Native features
12,651
Expression unit
GEO-supplied FPKM
3 samples in this species view
12,651 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.

Vervet GSE43013 PCA Scatter plot of 3 samples. Each point is keyboard focusable and labelled by accession and tissue. cae.lv.1 · Liver · PC1 -94.84 · PC2 -55.27 cae.kd.1 · Kidney · PC1 -33.25 · PC2 76.37 cae.br.1 · Brain · PC1 128.10 · PC2 -21.10
Observed ranges: PC1 -94.84 to 128.10; PC2 -55.27 to 76.37.

Tissue legend

  • Brain1
  • Kidney1
  • Liver1
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
cae.lv.1 ↗ GSM1054991 Liver 11,938 3.267e+7 13.5112
cae.kd.1 ↗ GSM1055041 Kidney 12,226 7.866e+7 24.9577
cae.br.1 ↗ GSM1055086 Brain 12,482 1.112e+8 33.8511
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-Val
    log1p variance
    43.3677
    mean native value
    93,676.8
    detected samples
    2/3
  2. 02
    tRNA-Phe
    log1p variance
    41.9976
    mean native value
    24,985.0
    detected samples
    1/3
  3. 03
    CAEG00000006725
    log1p variance
    19.3348
    mean native value
    13,264.6
    detected samples
    3/3
  4. 04
    CAEG00000012941
    log1p variance
    18.9299
    mean native value
    1,450.4
    detected samples
    3/3
  5. 05
    CAEG00000010419
    log1p variance
    18.8545
    mean native value
    615.0633
    detected samples
    1/3
  6. 06
    CAEG00000013938
    log1p variance
    18.3396
    mean native value
    3,323.2
    detected samples
    3/3
  7. 07
    CAEG00000007731
    log1p variance
    17.7934
    mean native value
    6,977.7
    detected samples
    3/3
  8. 08
    CAEG00000013901
    log1p variance
    16.9213
    mean native value
    1,604.4
    detected samples
    3/3
  9. 09
    CAEG00000012960
    log1p variance
    16.8385
    mean native value
    800.3124
    detected samples
    2/3
  10. 10
    CAEG00000000118
    log1p variance
    16.7208
    mean native value
    974.5313
    detected samples
    3/3
  11. 11
    CAEG00000013950
    log1p variance
    16.4320
    mean native value
    3,031.8
    detected samples
    3/3
  12. 12
    CAEG00000004012
    log1p variance
    16.2395
    mean native value
    7,501.6
    detected samples
    3/3
  13. 13
    CAEG00000010403
    log1p variance
    15.7322
    mean native value
    438.0322
    detected samples
    2/3
  14. 14
    CAEG00000013921
    log1p variance
    15.6606
    mean native value
    874.4940
    detected samples
    3/3
  15. 15
    CAEG00000002974
    log1p variance
    15.6416
    mean native value
    12,957.4
    detected samples
    3/3
  16. 16
    CAEG00000010353
    log1p variance
    15.5547
    mean native value
    356.7030
    detected samples
    3/3
  17. 17
    CAEG00000008119
    log1p variance
    15.2733
    mean native value
    1,334.2
    detected samples
    3/3
  18. 18
    CAEG00000013946
    log1p variance
    15.0950
    mean native value
    924.0100
    detected samples
    3/3
  19. 19
    CAEG00000013980
    log1p variance
    15.0122
    mean native value
    460.6878
    detected samples
    3/3
  20. 20
    CAEG00000010651
    log1p variance
    14.9505
    mean native value
    269.6890
    detected samples
    1/3
  21. 21
    CAEG00000010565
    log1p variance
    14.9248
    mean native value
    268.1437
    detected samples
    1/3
  22. 22
    CAEG00000010560
    log1p variance
    14.6861
    mean native value
    254.1000
    detected samples
    1/3
  23. 23
    CAEG00000007991
    log1p variance
    14.6408
    mean native value
    4,174.2
    detected samples
    3/3
  24. 24
    CAEG00000013899
    log1p variance
    14.4371
    mean native value
    597.9551
    detected samples
    3/3
  25. 25
    CAEG00000007727
    log1p variance
    14.4162
    mean native value
    10,728.0
    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

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