Within-species exploratory view · GSE43013

Mongolian gerbil native expression

Meriones unguiculatus

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
14,380
Expression unit
GEO-supplied FPKM
9 samples in this species view
14,380 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.

Mongolian gerbil GSE43013 PCA Scatter plot of 9 samples. Each point is keyboard focusable and labelled by accession and tissue. mun.lv.1 · Liver · PC1 -115.59 · PC2 -60.30 mun.lv.2 · Liver · PC1 -116.67 · PC2 -61.82 mun.lv.3 · Liver · PC1 -117.26 · PC2 -61.27 mun.kd.1 · Kidney · PC1 -20.41 · PC2 97.79 mun.kd.2 · Kidney · PC1 -18.38 · PC2 101.53 mun.kd.3 · Kidney · PC1 -18.93 · PC2 99.15 mun.br.1 · Brain · PC1 134.08 · PC2 -36.83 mun.br.2 · Brain · PC1 135.84 · PC2 -36.97 mun.br.3 · Brain · PC1 137.32 · PC2 -41.28
Observed ranges: PC1 -117.26 to 137.32; PC2 -61.82 to 101.53.

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
mun.lv.1 ↗ GSM1055015 Liver 13,104 936,693.7 9.1271
mun.lv.2 ↗ GSM1055016 Liver 13,038 922,880.3 8.8967
mun.lv.3 ↗ GSM1055017 Liver 13,005 947,886.4 8.8078
mun.kd.1 ↗ GSM1055063 Kidney 13,844 989,410.7 22.6910
mun.kd.2 ↗ GSM1055064 Kidney 13,758 1.085e+6 23.9539
mun.kd.3 ↗ GSM1055065 Kidney 13,839 1.018e+6 22.7447
mun.br.1 ↗ GSM1055108 Brain 14,162 888,226.1 26.0869
mun.br.2 ↗ GSM1055109 Brain 14,171 910,562.1 26.3110
mun.br.3 ↗ GSM1055110 Brain 14,125 832,398.3 24.8632
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
    MUNG00000007887
    log1p variance
    17.4937
    mean native value
    46,553.8
    detected samples
    9/9
  2. 02
    MUNG00000016417
    log1p variance
    15.9103
    mean native value
    1,539.5
    detected samples
    6/9
  3. 03
    MUNG00000000710
    log1p variance
    15.5188
    mean native value
    5,058.5
    detected samples
    9/9
  4. 04
    MUNG00000005567
    log1p variance
    15.0113
    mean native value
    2,857.3
    detected samples
    8/9
  5. 05
    MUNG00000000741
    log1p variance
    14.7446
    mean native value
    2,642.0
    detected samples
    9/9
  6. 06
    MUNG00000000010
    log1p variance
    14.6684
    mean native value
    4,467.4
    detected samples
    9/9
  7. 07
    MUNG00000018838
    log1p variance
    14.6072
    mean native value
    1,693.0
    detected samples
    8/9
  8. 08
    MUNG00000015860
    log1p variance
    14.2231
    mean native value
    1,545.4
    detected samples
    9/9
  9. 09
    MUNG00000009960
    log1p variance
    14.1280
    mean native value
    976.9101
    detected samples
    7/9
  10. 10
    MUNG00000018214
    log1p variance
    14.0878
    mean native value
    1,472.5
    detected samples
    8/9
  11. 11
    MUNG00000000707
    log1p variance
    13.9730
    mean native value
    2,146.4
    detected samples
    9/9
  12. 12
    MUNG00000002122
    log1p variance
    13.7707
    mean native value
    854.2747
    detected samples
    9/9
  13. 13
    MUNG00000000740
    log1p variance
    13.4628
    mean native value
    1,655.5
    detected samples
    9/9
  14. 14
    MUNG00000005551
    log1p variance
    13.3471
    mean native value
    987.4498
    detected samples
    8/9
  15. 15
    MUNG00000015844
    log1p variance
    13.1633
    mean native value
    1,874.3
    detected samples
    9/9
  16. 16
    MUNG00000001388
    log1p variance
    13.1499
    mean native value
    2,027.2
    detected samples
    9/9
  17. 17
    MUNG00000015891
    log1p variance
    12.8857
    mean native value
    2,329.7
    detected samples
    9/9
  18. 18
    MUNG00000016493
    log1p variance
    12.8611
    mean native value
    990.1603
    detected samples
    7/9
  19. 19
    MUNG00000000708
    log1p variance
    12.7031
    mean native value
    793.5057
    detected samples
    8/9
  20. 20
    MUNG00000000027
    log1p variance
    12.6017
    mean native value
    1,184.7
    detected samples
    9/9
  21. 21
    MUNG00000012695
    log1p variance
    12.3793
    mean native value
    541.3855
    detected samples
    9/9
  22. 22
    MUNG00000009113
    log1p variance
    12.3757
    mean native value
    2,922.4
    detected samples
    9/9
  23. 23
    MUNG00000008995
    log1p variance
    12.2543
    mean native value
    486.1643
    detected samples
    9/9
  24. 24
    MUNG00000000016
    log1p variance
    12.1565
    mean native value
    1,782.3
    detected samples
    9/9
  25. 25
    MUNG00000000749
    log1p variance
    12.1342
    mean native value
    1,768.3
    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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