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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1400 to 1449 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
1400 ATF7 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] 218.667 214.118 1.02125
1401 ATF2 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] 218.657 214.11 1.02124
1402 MCC colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] 209.682 205.329 1.0212
1403 ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] 184.656 180.823
1404 SF3B4 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] 232.752 237.65 1.02104
1405 EIF3C eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 245.532 240.483 1.021
1406 NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] 212.833 208.456
1407 WDFY1 wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] 206.104 210.424 1.02096
1408 STIM1 stromal interaction molecule 1 precursor. [swissprot;acc:q13586] 206.102 210.42 1.02095
1409 MED30 trap/mediator complex component trap25. [refseq;acc:nm_080651]
1410 WDFY2 wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] 206.1 210.417
1411 PAK4 serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] 206.102 210.42
1412 REEP5 polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]
1413 ACADM acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]
1414 REEP6 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]
1415 STIM2 stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]
1416 PAK7 serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]
1417 CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] 203.979 208.229 1.02084
1418 CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]
1419 SLC3A1 neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]
1420 ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
1421 ASAH1 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] 207.076 211.391
1422 CPA1 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 203.979 208.229
1423 no value cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] 221.152 216.659 1.02074
1424 ATP1A1 sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] 214.717 219.157 1.02068
1425 CTSL2 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911]
1426 CTSL1 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]
1427 ATP1A3 sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637]
1428 ATP1A2 sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]
1429 WDR26 wd repeat domain 26. [refseq;acc:nm_025160] 213.351 217.74 1.02057
1430 DUT deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [swissprot;acc:p33316] 187.114 190.925 1.02037
1431 RAD23A uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725] 220.987 225.468 1.02028
1432 PSMD4 26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
1433 OCRL inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968]
1434 RAD23B uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727]
1435 no value myosin vi. [swissprot;acc:q9um54]
1436 EVI5L similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] 218.829 214.493 1.02022
1437 EVI5 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
1438 PGGT1B geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609] 225.039 229.573 1.02015
1439 FADS3 fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727]
1440 SMAD4 mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485]
1441 FADS2 fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]
1442 no value fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]
1443 GLUD2 glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448] 203.908 207.998 1.02006
1444 GLUDP5 glutamate dehydrogenase 1, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p00367]
1445 PCF11 pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913] 134.233 136.922 1.02003
1446 HSPB1 heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792] 221.817 226.23 1.01989
1447 POLE3 dna polymerase epsilon p17 subunit (dna polymerase epsilon subunit 3) (chromatin accessibility complex 17) (huchrac17) (chrac-17). [swissprot;acc:q9nrf9] 250.854 255.842 1.01988
1448 ZMPSTE24 caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] 226.532 222.117
1449 TNPO3 transportin-sr; importin 12. [refseq;acc:nm_012470] 225.305 229.766 1.0198

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/