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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1425 to 1474 of 8289 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Interaction Map
red
green
network_comparison
713 DDX4 dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0] Low confidence 206.262 200.71 1.02766
EIF3M dendritic cell protein. [refseq;acc:nm_006360] High confidence 223.121 211.685 1.05402
714 CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]
SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Low confidence 152.572 148.47 1.02763
715 CPN1 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] High confidence 223.121 211.685 1.05402
GARS glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] Low confidence 203.107 197.646 1.02763
716 CPZ cpz gene product. [refseq;acc:nm_003652] High confidence 223.121 211.685 1.05402
EEF1D elongation factor 1-delta (ef-1-delta) (antigen ny-co-4). [swissprot;acc:p29692] Low confidence 203.552 198.081 1.02762
717 BTF3 transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] 204.133 198.652 1.02759
CPE carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] High confidence 223.121 211.685 1.05402
718 ARPC1B arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] Low confidence 201.612 196.213 1.02752
CPXM1 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] High confidence 223.121 211.685 1.05402
719 NOL5A nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 247.769 235.074 1.054
STUB1 stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] Low confidence 199.172 193.841 1.0275
720 POLE dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 204.279 198.814 1.02749
RPLP2 60s acidic ribosomal protein p2. [swissprot;acc:p05387] High confidence 231.92 244.435 1.05396
721 EXOC5 exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] 214.765 203.8 1.0538
SNX16 sorting nexin 16. [swissprot;acc:p57768] Low confidence 203.411 197.971 1.02748
722 IGF2BP1 igf-ii mrna-binding protein 1. [refseq;acc:nm_006546] 205.571 200.075 1.02747
TREH trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] High confidence 217.952 206.902 1.05341
723 no value histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 244.842 232.577 1.05274
PARN poly(a)-specific ribonuclease (deadenylation nuclease); deadenylation nuclease. [refseq;acc:nm_002582] Low confidence 203.779 198.331 1.02747
724 no value dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] High confidence 244.842 232.577 1.05274
ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Low confidence 201.765 196.371 1.02747
725 IGF2BP3 igf-ii mrna-binding protein 3; kh domain containing protein overexpressed in cancer. [refseq;acc:nm_006547] 205.563 200.075 1.02743
MVK mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] High confidence 235.296 247.673 1.0526
726 DDX39 dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804] Low confidence 192.552 187.412 1.02743
FTSJ3 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] High confidence 244.495 232.419 1.05196
727 ARPC1A actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Low confidence 201.571 196.189 1.02743
NUAK1 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] High confidence 208.873 219.71 1.05188
728 B3GNT1 n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505] 208.874 219.708 1.05187
IGF2BP2 igf-ii mrna-binding protein 2. [refseq;acc:nm_006548] Low confidence 205.561 200.075 1.02742
729 no value huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076] High confidence 208.874 219.708 1.05187
MRPS16 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Low confidence 205.65 200.165 1.0274
730 MRPS26 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] 206.555 201.05 1.02738
TIMM10 mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8] High confidence 208.874 219.708 1.05187
731 FH fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]
PARS2 similar to trna synthetase class ii. [refseq;acc:nm_152268] Low confidence 203.316 197.904 1.02735
732 PPP1R3C protein phosphatase 1, regulatory (inhibitor) subunit 5; phosphatase 1, regulatory inhibitor subunit 5. [refseq;acc:nm_005398] 203.592 198.172
SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] High confidence 124.434 118.318 1.05169
733 ACADVL acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748] 164 155.961 1.05154
MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Low confidence 204.098 198.67 1.02732
734 no value presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] High confidence 232.601 244.534 1.0513
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Low confidence 153.764 149.678 1.0273
735 LIG1 dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] 204.123 198.699
RANP1 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] High confidence 232.601 244.534 1.0513
736 no value presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Low confidence 202.639 197.261 1.02726
737 OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 179.918 175.156 1.02719
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] High confidence 125.526 119.402 1.05129

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/