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 2758 to 2807 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
1379 RERE arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] Divided 218.47 213.875 1.02148
1380 no value myosin vi. [swissprot;acc:q9um54] Subtracted 220.987 225.468 4.481
USP8 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] Divided 218.47 213.876 1.02148
1381 MPP2 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Subtracted 228.513 232.983 4.47
ROD1 rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156] Divided 218.47 213.876 1.02148
1382 PPP2R5E serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] Subtracted 130.066 134.527 4.461
PTBP2 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] Divided 218.47 213.876 1.02148
1383 AAK1 adaptor-associated kinase 1. [refseq;acc:nm_014911]
CCNG2 cyclin g2. [swissprot;acc:q16589] Subtracted 130.066 134.527 4.461
1384 ATN1 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Divided 218.471 213.876 1.02148
CCNG1 cyclin g1 (cyclin g). [swissprot;acc:p51959] Subtracted 130.066 134.527 4.461
1385 no value dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Divided 218.47 213.875 1.02148
PPP2R5A serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Subtracted 130.066 134.527 4.461
1386 ARHGAP21 rho-gtpase activating protein 10. [refseq;acc:nm_020824] Divided 218.47 213.876 1.02148
TNPO3 transportin-sr; importin 12. [refseq;acc:nm_012470] Subtracted 225.305 229.766 4.461
1387 BOLA2B my016 protein. [sptrembl;acc:q9h3k6] 224.755 229.2 4.445
SALL1 sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] Divided 218.47 213.875 1.02148
1388 ATP1A1 sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Subtracted 214.717 219.157 4.44
SALL4 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Divided 218.471 213.876 1.02148
1389 BCKDHB 2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953] 218.47 213.875
CTSL2 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Subtracted 214.717 219.157 4.44
1390 CNOT4 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] Divided 218.47 213.875 1.02148
CTSL1 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] Subtracted 214.717 219.157 4.44
1391 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]
PICALM phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Divided 218.47 213.875 1.02148
1392 ATP1A2 sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Subtracted 214.717 219.157 4.44
SNAP91 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] Divided 218.471 213.876 1.02148
1393 BRAF b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Subtracted 130.289 134.713 4.424
RC3H2 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Divided 218.47 213.875 1.02148
1394 PTBP1 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]
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] Subtracted 226.532 222.117 4.415
1395 GAS7 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] Divided 218.47 213.876 1.02148
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] Subtracted 221.817 226.23 4.413
1396 EYA1 eyes absent homolog 1. [swissprot;acc:q99502] Divided 218.463 213.872 1.02147
NCK1 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Subtracted 205.185 200.784 4.401
1397 HSPB8 alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] 221.804 226.194 4.39
RPS8 40s ribosomal protein s8. [swissprot;acc:p09058] Divided 218.64 214.049 1.02145
1398 EYA4 eyes absent homolog 4. [swissprot;acc:o95677] 218.449 213.864 1.02144
WDR26 wd repeat domain 26. [refseq;acc:nm_025160] Subtracted 213.351 217.74 4.389
1399 EYA2 eyes absent homolog 2. [swissprot;acc:o00167] Divided 218.417 213.848 1.02137
MPP6 maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Subtracted 228.469 232.855 4.386
1400 ATF7 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] Divided 218.667 214.118 1.02125
PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Subtracted 170.28 165.898 4.382
1401 ATF2 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] Divided 218.657 214.11 1.02124
NR6A1 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Subtracted 212.833 208.456 4.377
1402 MCC colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Divided 209.682 205.329 1.0212
Subtracted 4.353
1403 CPSF2 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 110.2 114.552 4.352
ECHS1 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] Divided 184.656 180.823 1.0212
1404 KRR1 hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043] Subtracted 242.181 237.834 4.347

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/