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 2901 to 2950 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
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] Divided 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
SNX16 sorting nexin 16. [swissprot;acc:p57768] Subtracted Low confidence 203.411 197.971 5.44
XAB2 xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] High confidence 222.825 211.966 10.859
727 ARPC1A actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747] Divided Low confidence 201.571 196.189 1.02743
EPS8L2 epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] Subtracted 206.435 201.001 5.434
NUAK1 probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285] Divided High confidence 208.873 219.71 1.05188
Subtracted 10.837
728 ALDH3B2 aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448] Low confidence 209.59 215.023 5.433
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] Divided High confidence 208.874 219.708 1.05187
Subtracted 10.834
IGF2BP2 igf-ii mrna-binding protein 2. [refseq;acc:nm_006548] Divided 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
Subtracted 10.834
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 5.428
MRPS16 28s ribosomal protein s16, mitochondrial precursor (mrp-s16) (cgi- 132). [swissprot;acc:q9y3d3] Divided 205.65 200.165 1.0274
730 no value u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted 201.325 195.897 5.428
MRPS26 28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8] Divided 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
Subtracted 10.834
731 FBXL10 protein containing cxxc domain 2. [refseq;acc:nm_032590] Low confidence 202.951 208.378 5.427
FH fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954] Divided High confidence 208.874 219.708 1.05187
Subtracted 10.834
PARS2 similar to trna synthetase class ii. [refseq;acc:nm_152268] Divided Low confidence 203.316 197.904 1.02735
732 no value translin. [swissprot;acc:q15631] Subtracted High confidence 224.385 235.131 10.746
G3BP2 ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Low confidence 210.933 216.358 5.425
PPP1R3C protein phosphatase 1, regulatory (inhibitor) subunit 5; phosphatase 1, regulatory inhibitor subunit 5. [refseq;acc:nm_005398] Divided 203.592 198.172 1.02735
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
LIG1 dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] Subtracted Low confidence 204.123 198.699 5.424
MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Divided 204.098 198.67 1.02732
TSNAX translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] Subtracted High confidence 224.385 235.131 10.746
734 no value presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8] Divided 232.601 244.534 1.0513
PQBP1 polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] Subtracted 224.385 235.131 10.746
SAR1B gtp-binding protein sar1b. [swissprot;acc:q9y6b6] Low confidence 201.401 195.979 5.422
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Divided 153.764 149.678 1.0273
735 HEMK1 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] Subtracted High confidence 229.045 218.343 10.702
LIG1 dna ligase i (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p18858] Divided Low confidence 204.123 198.699 1.0273
PPP1R3C protein phosphatase 1, regulatory (inhibitor) subunit 5; phosphatase 1, regulatory inhibitor subunit 5. [refseq;acc:nm_005398] Subtracted 203.592 198.172 5.42
RANP1 gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080] Divided High confidence 232.601 244.534 1.0513
736 no value presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
MAD1L1 mad1-like 1; mad1 (mitotic arrest deficient, yeast, homolog)-like 1; mitotic-arrest deficient 1, yeast, homolog-like 1; tumor protein p53 inducible protein 9. [refseq;acc:nm_003550] Subtracted Low confidence 208.017 202.601 5.416
N6AMT1 putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] High confidence 228.78 218.091 10.689
PDCD11 rrp5 protein homolog (programmed cell death protein 11). [swissprot;acc:q14690] Divided Low confidence 202.639 197.261 1.02726
737 AGPAT3 1-acyl-sn-glycerol-3-phosphate acyltransferase gamma (ec 2.3.1.51) (1- agp acyltransferase 3) (1-agpat 3) (lysophosphatidic acid acyltransferase-gamma) (lpaat-gamma) (1-acylglycerol-3-phosphate o- acyltransferase 3). [swissprot;acc:q9nrz7] Subtracted 192.166 186.751 5.415
EXOC6B exocyst complex component sec15b. [swissprot;acc:q9y2d4] High confidence 221.968 211.326 10.642
OTC ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] Divided Low confidence 179.918 175.156 1.02719
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] High confidence 125.526 119.402 1.05129
738 EPS8L1 epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] Low confidence 206.474 201.013 1.02717
EXOC6 exocyst complex component sec15a. [swissprot;acc:q8tag9] Subtracted High confidence 222.138 211.503 10.635

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/