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 Value Type Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2430 to 2479 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
608 Ranked no value histone h2b. [refseq;acc:nm_175055] 247.47 233.441 1.0601
Squared FDXR nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] 24560.6 29071.1 1.18365
Rooted SFRS11 splicing factor arginine/serine-rich 11 (arginine-rich 54 kda nuclear protein) (p54). [swissprot;acc:q05519] 59.6517 64.4642 1.08068
609 Measured B9D1 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 3886.62 3438.82 1.13022
Ranked no value histone h2b.s (h2b/s). [swissprot;acc:p57053] 247.47 233.441 1.0601
Squared PYCR2 pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] 12276.9 14526 1.1832
Rooted PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] 62.9281 67.99 1.08044
610 Measured KYNU kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] 8430.03 9518.11 1.12907
Ranked no value histone h2b.d (h2b/d). [swissprot;acc:q99877] 247.47 233.441 1.0601
Squared PYCR1 pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] 12347.6 14594.8 1.18199
Rooted CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 136.706 126.565 1.08012
611 Measured DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 5148.71 5811.74 1.12878
Ranked HIST3H3 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] 247.47 233.441 1.0601
Squared no value bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 23487.1 27726.3 1.18049
Rooted NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 51.0091 55.0909 1.08002
612 Measured EIF3I eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 3975.77 4485.05 1.1281
Ranked HIST1H2BA testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] 247.47 233.441 1.0601
Squared no value u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333] 18595.6 21936.3 1.17965
Rooted MYCL1 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 57.1949 61.7633 1.07987
613 Measured no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] 3975.77 4485.05 1.1281
Ranked histone h2b.e (h2b/e). [swissprot;acc:q99879] 247.47 233.441 1.0601
Squared ARD1A n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 17550.2 20701.1 1.17954
Rooted MYCN n-myc proto-oncogene protein. [swissprot;acc:p04198] 57.1971 61.7626 1.07982
614 Measured SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 11222.2 9948.93 1.12798
Ranked HOXA10 homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] 214.257 202.125 1.06002
Squared COPB2 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] 51527.6 43689.1 1.17942
Rooted GABPA ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 57.2007 61.7615 1.07973
615 Measured CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 11222.2 9948.93 1.12798
Ranked HOXB9 homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] 214.257 202.132 1.05999
Squared COPG coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] 51527.6 43689.1 1.17942
Rooted no value ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 57.2007 61.7615 1.07973
616 Measured CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 11222.2 9948.93 1.12798
Ranked HOXA9 homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] 214.257 202.132 1.05999
Squared COPZ1 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] 51527.6 43689.1 1.17942
Rooted NDUFS8 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] 57.2007 61.7615 1.07973
617 Measured DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] 5162.52 5822.47 1.12783
Ranked HOXC9 homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] 214.257 202.135 1.05997
Squared ARCN1 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] 51527.6 43689.1 1.17942
Rooted ELOVL1 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] 57.2008 61.7614 1.07973
618 Measured NME3 nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] 7878.27 8879.08 1.12703
Ranked GABRG3 gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] 214.256 202.139 1.05994
Squared PPIE peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] 51527.6 43689.1 1.17942
Rooted MYC myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] 57.208 61.7592 1.07956
619 Measured NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 3879.99 4371.24 1.12661
Ranked FOXG1 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 214.256 202.139 1.05994
Squared COPZ2 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] 51527.6 43689.1 1.17942
Rooted EIF3M dendritic cell protein. [refseq;acc:nm_006360] 63.847 68.8873 1.07894
620 Measured FTH1 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 6227.87 7012.9 1.12605
Ranked GABRG1 gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3] 214.256 202.14 1.05994
Squared HOXD9 homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] 32208.8 37986.6 1.17939

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
- Hugo is the HGNC identifier if it exists
- 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/