Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 351 to 400 of 77072 in total
Rank
description
Value Type
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
11 trypsin iii precursor (ec 3.4.21.4) (brain trypsinogen) (mesotrypsinogen) (trypsin iv). [swissprot;acc:p35030] Ranked Subtracted Low confidence 1 304.548 246.824 57.724
Rooted Divided 32.2231 47.928 1.48738
12 adp,atp carrier protein, liver isoform t2 (adp/atp translocase 3) (adenine nucleotide translocator 3) (ant 3). [swissprot;acc:p12236] Subtracted High confidence 0 21.3967 34.6716 13.2749
anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [refseq;acc:nm_003801] Ranked Divided Low confidence 3190 1933 1.65028
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Squared Subtracted High confidence 1.73869 19295.9 19294.2
bax inhibitor-1 (bi-1) (testis enhanced gene transcript). [swissprot;acc:p55061] Low confidence 1 281799 228277 53522
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Rooted High confidence 80.4705 101.526 21.0555
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Low confidence 0 23.8747 11.7898 12.0849
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured High confidence 5629.62 7099.51 1469.89
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Divided 1 398.5 1281.5 3.21581
Squared 37.5863 388.696 10.3414
Rooted 19.9625 35.798 1.79326
folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Ranked 0 9429.18 5208.84 1.81023
gbp protein isoform a. [refseq;acc:nm_017870] Measured Low confidence 1 1921.96 2954.24 1.5371
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Ranked Subtracted High confidence 266.856 336.233 69.377
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured Low confidence 15464.1 17572.7 2108.6
hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8] Divided High confidence 0 199.249 5.71669 34.8539
Ranked Subtracted Low confidence 14592 21113.7 6521.7
Squared Divided 23.4957 0.0297673 789.312
Rooted 10.3085 1.2188 8.45791
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Squared Subtracted High confidence 1 219048 129762 89286
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Divided Low confidence 106226 192141 1.80879
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Measured 0 859 58 14.8103
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted High confidence 1 34190.9 40795.8 6604.9
nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Squared Low confidence 0 10489.8 23426.5 12936.7
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] Ranked Divided High confidence 1 337 232 1.45259
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Subtracted 0 19403 11267 8136
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Squared Divided 0.00001 0.437633 43763.3
Rooted 6.55744 655744
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Measured Subtracted Low confidence 31122 30022.4 1099.6
trypsin i precursor (ec 3.4.21.4) (cationic trypsinogen). [swissprot;acc:p07477] Ranked 1 304.359 246.737 57.622
Rooted Divided 32.2966 47.9763 1.48549
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Ranked 37.3475 28.5242 1.30933
Rooted Subtracted 187.325 204.557 17.232
13 25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528] Divided 39.2301 52.5277 1.33896
adenomatous polyposis coli like. [refseq;acc:nm_005883] Subtracted 0 27.8758 39.3522 11.4764
adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [swissprot;acc:q9np61] Measured Divided High confidence 1363 47 29
Subtracted 1316
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Rooted 1 80.4705 101.526 21.0555
cab2. [refseq;acc:nm_033419] 0 0 13.1909 13.1909
carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Squared Divided Low confidence 1 395912 242799 1.63062
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Measured High confidence 398.5 1281.5 3.21581
Squared 37.5863 388.696 10.3414
Rooted 19.9625 35.798 1.79326
dok-like protein. [refseq;acc:nm_024872] Squared 0 0.289941 0.00001 28994.1
Rooted 5.91608 591608
dystrophin. [swissprot;acc:p11532] Ranked Subtracted 10232.5 18054.8 7822.3
fk506-binding protein 6 (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (36 kda fk506 binding protein) (fkbp- 36) (immunophilin fkbp36). [swissprot;acc:o75344] Measured Divided Low confidence 8.11997 115.385 14.21
Ranked Subtracted 20324.1 14746.1 5578
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] High confidence 1 266.856 336.233 69.377

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/