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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 373 to 422 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
47 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Rooted Subtracted 137.446 120.823 16.623
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Ranked 350 290 60
trs85 homolog. [swissprot;acc:q9y2l5] Measured 24896.4 20431.7 4464.7
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Squared Divided 98517.9 56927.2 1.73059
48 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Measured 779.167 1390.33 1.78438
gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] Ranked 65.4586 83.0461 1.26868
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared 6300.2 10703.5 1.69891
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Rooted Subtracted 137.446 120.823 16.623
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Squared 210199 136638 73561
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Rooted Divided 27.7254 44.0299 1.58807
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] Ranked Subtracted 350 290 60
wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Measured 24806.9 20369.9 4437
49 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Squared Divided 28994.2 17134.8 1.69212
beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] Ranked 133 105 1.26667
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] Measured Subtracted 24806.9 20369.9 4437
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Squared 201896 131906 69990
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Ranked 350 290 60
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Rooted Divided 27.7254 44.0299 1.58807
melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted 137.446 120.823 16.623
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] Measured Divided 779.167 1390.33 1.78438
50 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Ranked 133 105 1.26667
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Measured Subtracted 24473.9 20127.8 4346.1
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked 350 290 60
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Squared 173408 242989 69581
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Rooted Divided 27.7254 44.0299 1.58807
melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Subtracted 137.446 120.823 16.623
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Measured Divided 779.167 1390.33 1.78438
putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Squared 28994.2 17134.8 1.69212
51 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked Subtracted 350 290 60
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 4160.4
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted 137.446 120.823 16.623
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Squared 173408 242989 69581
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted Divided 27.7254 44.0299 1.58807
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 1.78438
spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 105 1.26667
52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 779.167 1390.33 1.78438
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 23422.4 19380.3 4042.1
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 242989 69581
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 120.823 16.623
neuralized-like. [refseq;acc:nm_004210] Divided 27.9107 44.1656 1.58239
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 17134.8 1.69212
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked Subtracted 350 290 60
53 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Measured Divided 779.167 1390.33 1.78438
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared Subtracted 173408 242989 69581
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Ranked 318.982 259.004 59.978
Rooted Divided 30.8986 46.4619 1.50369
necdin. [swissprot;acc:q99608] Subtracted 137.446 120.823 16.623
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 4030.1

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/