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 1844 to 1893 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
461 scratch; scratch 1. [refseq;acc:nm_031309] Divided 0 12164.9 12358.1 1.01588
462 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] Subtracted 10076.4 9928.08 148.32
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Divided 12189.6 12378.3 1.01548
dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Subtracted 1 236.662 252.708 16.046
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Divided 254.434 236.224 1.07709
463 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 0 5558.06 5473.99 1.01536
dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 1 238.921 257.327 1.07704
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Subtracted 0 11319.2 11463 143.8
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] 1 223.648 207.62 16.028
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] Divided 210.578 226.764 1.07686
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 0 10076.4 9928.08 1.01494
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Subtracted 1 223.648 207.62 16.028
ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986] 0 15920 15780.2 139.8
465 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 1 224.662 240.673 16.011
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Divided 248.152 267.226 1.07686
transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724] 0 9482.68 9620.66 1.01455
Subtracted 137.98
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306] Divided 1 248.152 267.226 1.07686
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Subtracted 0 15155.8 15031.7 124.1
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Divided 1543 1521 1.01446
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Subtracted 1 225.661 209.651 16.01
467 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Divided 248.152 267.226 1.07686
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Subtracted 248.56 232.579 15.981
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261] Divided 0 21205 20914 1.01391
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Subtracted 15155.8 15031.7 124.1
468 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 1 237.627 253.604 15.977
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001] Divided 0 21205 20914 1.01391
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] 1 248.152 267.226 1.07686
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Subtracted 0 11290.1 11167.6 122.5
469 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322] Divided 1 248.152 267.226 1.07686
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745] 0 21205 20914 1.01391
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Subtracted 1251 1373 122
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 15.971
470 h2a histone family, member j isoform 1. [refseq;acc:nm_018267] Divided 0 21205 20914 1.01391
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Subtracted 1 224.535 240.476 15.941
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Divided 248.152 267.226 1.07686
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Subtracted 0 12223.8 12127.5 96.3
471 galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Divided 11319.2 11463 1.0127
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] 1 248.152 267.226 1.07686
uridine kinase-like 1. [swissprot;acc:q9nwz5] Subtracted 0 11554.3 11462.4 91.9
zinc finger-like protein 9. [refseq;acc:nm_033414] 1 250.942 235.004 15.938
472 membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]
peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753] Divided 0 7080.27 7165.6 1.01205
rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952] Subtracted 21970 21880 90
thymic stromal co-transporter. [refseq;acc:nm_033051] Divided 1 248.152 267.226 1.07686
473 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Subtracted 0 10156.4 10243.1 86.7
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098] Divided 816 825 1.01103
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Subtracted 1 250.942 235.004 15.938
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Divided 225.661 209.651 1.07637
474 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] 0 11290.1 11167.6 1.01097

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/