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 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
470 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] Rooted 1 60.0148 65.6429 1.09378
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] 0 18.7853 18.9683 1.00974
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 1 10418.3 8641.84 1.20557
471 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Ranked 0 11319.2 11463 1.0127
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 1 248.152 267.226 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
phosphoglycerate kinase, testis specific (ec 2.7.2.3). [swissprot;acc:p07205] Squared 28188.7 33982.7 1.20554
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Rooted 0 93.5322 92.7071 1.0089
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Squared 6607.52 6525.61 1.01255
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Measured 3855.78 3825.73 1.00785
vav-2 protein. [swissprot;acc:p52735] Rooted 1 66.088 72.2597 1.09339
472 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] Squared 0 6605.9 6524 1.01255
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4] Rooted 110.816 111.772 1.00863
gamma enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (neural enolase) (nse) (enolase 2). [swissprot;acc:p09104] Squared 1 28190.4 33984.1 1.20552
histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] Measured 0 3889.5 3919.25 1.00765
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Ranked 7080.27 7165.6 1.01205
sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Measured 1 9649.61 11053.5 1.14549
thymic stromal co-transporter. [refseq;acc:nm_033051] Ranked 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
473 40s ribosomal protein s3a. [swissprot;acc:p49241] Squared 0 8653.02 8550.86 1.01195
beta enolase (ec 4.2.1.11) (2-phospho-d-glycerate hydro-lyase) (skeletal muscle enolase) (mse) (enolase 3). [swissprot;acc:p13929] 1 28190.4 33984.1 1.20552
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] Ranked 0 816 825 1.01103
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Measured 3889.5 3919.25 1.00765
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429] Rooted 110.861 111.817 1.00862
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Ranked 1 225.661 209.651 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 26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232] 0 2281.12 2263.85 1.00763
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 1 28190.4 33984.1 1.20552
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Rooted 62.574 68.4128 1.09331
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6] 0 110.799 111.754 1.00862
leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735] Squared 58677.8 58207.8 1.00807
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Ranked 11290.1 11167.6 1.01097
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 1 226.789 210.818 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
475 60s ribosomal protein l18a. [swissprot;acc:q02543] Squared 0 9310.69 9385.52 1.00804
adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559] Ranked 18667 18500 1.00903
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652] Measured 2319.24 2335.98 1.00722
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Rooted 1 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
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497] Rooted 0 110.625 111.576 1.0086
phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558] Squared 1 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
476 60s ribosomal protein l39. [swissprot;acc:p02404] Squared 0 10474.5 10558.6 1.00803
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Ranked 8403 8329 1.00888
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655] Measured 1362.55 1372.31 1.00716
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13] Rooted 110.543 111.493 1.00859
neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Measured 1 9649.61 11053.5 1.14549
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Ranked 226.681 210.814 1.07527
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Rooted 62.574 68.4128 1.09331

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/