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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene 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
description
Network Comparison Type
red
green
network_comparison
1379 uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727] Subtracted 220.987 225.468 4.481
1380 myosin vi. [swissprot;acc:q9um54]
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 maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Subtracted 228.513 232.983 4.47
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 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
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
1383 adaptor-associated kinase 1. [refseq;acc:nm_014911] Divided 218.47 213.876 1.02148
cyclin g2. [swissprot;acc:q16589] Subtracted 130.066 134.527 4.461
1384 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] Divided 218.471 213.876 1.02148
cyclin g1 (cyclin g). [swissprot;acc:p51959] Subtracted 130.066 134.527 4.461
1385 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] Divided 218.47 213.875 1.02148
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 rho-gtpase activating protein 10. [refseq;acc:nm_020824] Divided 218.47 213.876 1.02148
transportin-sr; importin 12. [refseq;acc:nm_012470] Subtracted 225.305 229.766 4.461
1387 my016 protein. [sptrembl;acc:q9h3k6] 224.755 229.2 4.445
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 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 218.471 213.876
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
1389 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] Divided 218.47 213.875 1.02148
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] Subtracted 214.717 219.157 4.44
1390 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]
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
1391 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492]
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Subtracted 214.717 219.157 4.44
1392 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
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
1393 b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 130.289 134.713 4.424
membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] Divided 218.47 213.875 1.02148
1394 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
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] Divided 218.47 213.875 1.02148
1395 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] 213.876
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 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] 205.185 200.784 4.401
eyes absent homolog 1. [swissprot;acc:q99502] Divided 218.463 213.872 1.02147
1397 40s ribosomal protein s8. [swissprot;acc:p09058] 218.64 214.049 1.02145
alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1] Subtracted 221.804 226.194 4.39
1398 eyes absent homolog 4. [swissprot;acc:o95677] Divided 218.449 213.864 1.02144
wd repeat domain 26. [refseq;acc:nm_025160] Subtracted 213.351 217.74 4.389
1399 eyes absent homolog 2. [swissprot;acc:o00167] Divided 218.417 213.848 1.02137
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Subtracted 228.469 232.855 4.386
1400 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
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Subtracted 170.28 165.898 4.382
1401 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
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 colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] Divided 209.682 205.329 1.0212
Subtracted 4.353
1403 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 110.2 114.552 4.352
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 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
- 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/