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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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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 3930 to 3979 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
983 pbk1 protein. [sptrembl;acc:o76021] Ranked 243.312 235.353 1.03382
protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760] Squared 31010.8 35677.6 1.15049
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Measured 6654.42 7296.51 1.09649
984 bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] Rooted 56.1854 53.2272 1.05558
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Measured 6362.64 6976.1 1.09642
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Ranked 116.71 120.654 1.03379
steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718] Squared 59338.5 68268.3 1.15049
985 integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7] Measured 6362.64 6976.1 1.09642
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Squared 22569.9 25956.6 1.15005
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Ranked 233.402 225.782 1.03375
tyrosinase precursor (ec 1.14.18.1) (monophenol monooxygenase) (tumor rejection antigen ab) (sk29-ab) (lb24-ab). [swissprot;acc:p14679] Rooted 61.9502 65.389 1.05551
986 adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] 62.4582 65.9096 1.05526
exocyst complex component sec5. [swissprot;acc:q96kp1] Ranked 116.771 120.707 1.03371
integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Measured 6362.64 6976.1 1.09642
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Squared 22569.9 25956.6 1.15005
987 maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368] Measured 6660.04 7301.81 1.09636
methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5] Squared 20465.9 23535.3 1.14998
serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464] Ranked 218.459 211.338 1.03369
vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953] Rooted 62.4582 65.9096 1.05526
988 adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] Squared 18082.5 20792.7 1.14988
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Ranked 218.461 211.343 1.03368
ubiquitin-conjugating enzyme e2 n (ec 6.3.2.19) (ubiquitin-protein ligase n) (ubiquitin carrier protein n) (ubc13) (bendless-like ubiquitin conjugating enzyme). [swissprot;acc:q16781] Measured 6229.69 6829.58 1.0963
989 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Rooted 67.7394 71.4737 1.05513
kccr13l. [refseq;acc:nm_139179] Squared 23339.9 26834.1 1.14971
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Ranked 218.462 211.345 1.03367
signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843] Measured 11743.3 10712.3 1.09624
990 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Ranked 243.297 235.373 1.03367
dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Measured 5147.9 5641.25 1.09584
dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609] Squared 23339.9 26834.1 1.14971
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Rooted 64.0581 67.5829 1.05503
991 aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] Squared 26705.9 30699 1.14952
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Ranked 203.381 196.76 1.03365
transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595] Measured 6472.38 7092.65 1.09583
u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566] Rooted 52.2349 55.1039 1.05492
992 lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [swissprot;acc:q15046] Squared 18885.2 21708.3 1.14949
mstp028 protein. [refseq;acc:nm_031954] Rooted 61.7824 65.1711 1.05485
putative sialoglycoprotease type 2. [refseq;acc:nm_022353] Measured 5393.37 5909.47 1.09569
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Ranked 218.468 211.357 1.03364
993 arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815] Measured 6499.89 7121.77 1.09568
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Squared 29881.4 34348 1.14948
pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Ranked 211.071 204.205 1.03362
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Rooted 61.7884 65.1721 1.05476
994 interleukin-4 induced protein 1 precursor (fig-1 protein). [swissprot;acc:q96rq9] Measured 5800.95 6355.71 1.09563
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Ranked 116.845 120.772 1.03361
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Squared 18761.8 21564.5 1.14938
tumor necrosis factor, alpha-induced protein 1, endothelial (b12 protein). [swissprot;acc:q13829] Rooted 61.7917 65.1727 1.05472
995 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] Measured 5778.65 6328.56 1.09516
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Squared 25141.4 28896.8 1.14937
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Ranked 219.656 212.547 1.03345

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/