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 4858 to 4907 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
608 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Squared Subtracted 16120.1 20665.7 4545.6
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Measured 2234.68 2978.53 743.85
histone h2b. [refseq;acc:nm_175055] Ranked Divided 247.47 233.441 1.0601
nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Squared 24560.6 29071.1 1.18365
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Measured 4510.61 5098.74 1.13039
splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] Rooted 59.6517 64.4642 1.08068
Subtracted 4.8125
609 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] 74.3877 79.1931 4.8054
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] Measured Divided 3886.62 3438.82 1.13022
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Ranked Subtracted 226.523 213.786 12.737
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Measured 2234.73 2978.57 743.84
histone h2b.s (h2b/s). [swissprot;acc:p57053] Ranked Divided 247.47 233.441 1.0601
pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Rooted 62.9281 67.99 1.08044
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Squared 12276.9 14526 1.1832
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Subtracted 16120.1 20665.7 4545.6
610 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Rooted 74.3557 79.1513 4.7956
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] Divided 136.706 126.565 1.08012
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Measured Subtracted 2236.61 2980.35 743.74
histone h2b.d (h2b/d). [swissprot;acc:q99877] Ranked Divided 247.47 233.441 1.0601
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 8430.03 9518.11 1.12907
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Squared Subtracted 16120.1 20665.7 4545.6
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Divided 12347.6 14594.8 1.18199
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Ranked Subtracted 205.74 193.021 12.719
611 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Squared Divided 23487.1 27726.3 1.18049
dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Measured 5148.71 5811.74 1.12878
fibulin-2 precursor. [swissprot;acc:p98095] Subtracted 8670.59 9412.9 742.31
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Ranked Divided 247.47 233.441 1.0601
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Squared Subtracted 16120.1 20665.7 4545.6
steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474] Rooted 82.1645 86.9566 4.7921
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Ranked 228.986 216.276 12.71
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Rooted Divided 51.0091 55.0909 1.08002
612 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] Measured Subtracted 5480.24 6222.04 741.8
eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Divided 3975.77 4485.05 1.1281
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] Rooted 57.1949 61.7633 1.07987
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] Subtracted 50.2317 55.0025 4.7708
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Ranked 205.89 193.183 12.707
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Divided 247.47 233.441 1.0601
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Squared Subtracted 16120.1 20665.7 4545.6
u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] Divided 18595.6 21936.3 1.17965
613 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 16120.1 20665.7 4545.6
histone h2b.e (h2b/e). [swissprot;acc:q99879] Ranked Divided 247.47 233.441 1.0601
n-myc proto-oncogene protein. [swissprot;acc:p04198] Rooted 57.1971 61.7626 1.07982
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Squared 17550.2 20701.1 1.17954
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Ranked Subtracted 247.769 235.074 12.695
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] Rooted 50.2317 55.0025 4.7708
transforming protein rhoc (h9). [swissprot;acc:p08134] Measured 5480.24 6222.04 741.8
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Divided 3975.77 4485.05 1.1281
614 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Squared 51527.6 43689.1 1.17942
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Rooted 57.2007 61.7615 1.07973
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Ranked 214.257 202.125 1.06002

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/