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 3758 to 3807 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
470 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Measured Subtracted 5367.04 6233.12 866.08
Rooted Divided 60.0148 65.6429 1.09378
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] Squared 10418.3 8641.84 1.20557
471 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Ranked 248.152 267.226 1.07686
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Measured 9649.61 11053.5 1.14549
neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] Subtracted 5980.15 6843.48 863.33
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Rooted 74.8348 80.1352 5.3004
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared Divided 28188.7 33982.7 1.20554
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11] Subtracted 32174 37487.2 5313.2
vav-2 protein. [swissprot;acc:p52735] Rooted Divided 66.088 72.2597 1.09339
zinc finger-like protein 9. [refseq;acc:nm_033414] Ranked Subtracted 250.942 235.004 15.938
472 gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared Divided 28190.4 33984.1 1.20552
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Ranked Subtracted 250.942 235.004 15.938
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Measured 5246.01 6109.31 863.3
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Divided 9649.61 11053.5 1.14549
tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226] Squared Subtracted 32174 37487.2 5313.2
thymic stromal co-transporter. [refseq;acc:nm_033051] Ranked Divided 248.152 267.226 1.07686
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Rooted 50.3767 46.0753 1.09336
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Subtracted 58.7805 64.0772 5.2967
473 ad24 protein. [refseq;acc:nm_022451] 49.2558 54.5235 5.2677
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] Squared Divided 28190.4 33984.1 1.20552
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Ranked Subtracted 250.942 235.004 15.938
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Squared 27179.5 32490.8 5311.3
neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] Measured 5979.95 6842.78 862.83
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked Divided 225.661 209.651 1.07637
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Rooted 62.574 68.4128 1.09331
udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Measured 9649.61 11053.5 1.14549
474 alpha enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (non- neural enolase) (nne) (enolase 1) (phosphopyruvate hydratase). [swissprot;acc:p06733] Squared 28190.4 33984.1 1.20552
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Rooted Subtracted 50.0785 55.3215 5.243
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Divided 62.574 68.4128 1.09331
neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] Measured Subtracted 5979.94 6842.76 862.82
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Ranked 226.727 210.816 15.911
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Divided 226.789 210.818 1.07576
rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Measured 9649.61 11053.5 1.14549
transducin-like enhancer protein 2 (esg2). [swissprot;acc:q04725] Squared Subtracted 31479.4 36770.8 5291.4
475 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] Measured 5979.93 6842.72 862.79
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Rooted Divided 62.574 68.4128 1.09331
map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Measured 9649.61 11053.5 1.14549
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Squared 28192 33985.3 1.20549
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Ranked 226.727 210.816 1.07547
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Subtracted 236.964 252.86 15.896
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] Squared 31467.1 36752.2 5285.1
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Rooted 49.2848 54.5246 5.2398
476 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Squared 25533.3 30810.8 5277.5
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Measured Divided 9649.61 11053.5 1.14549
p66 alpha. [refseq;acc:nm_017660] Rooted Subtracted 93.8375 88.6044 5.2331
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Ranked Divided 226.681 210.814 1.07527
Subtracted 15.867
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Rooted Divided 62.574 68.4128 1.09331
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] Measured Subtracted 5067.02 5926.46 859.44

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/