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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2775 to 2824 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1388 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Divided 218.471 213.876 1.02148
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
splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] Divided 232.752 237.65 1.02104
1405 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 245.532 240.483 1.021
similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245] Subtracted 218.829 214.493 4.336
1406 ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Divided 212.833 208.456 1.021
1407 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
Subtracted 4.32
1408 stromal interaction molecule 1 precursor. [swissprot;acc:q13586] Divided 206.102 210.42 1.02095
Subtracted 4.318
1409 trap/mediator complex component trap25. [refseq;acc:nm_080651] Divided 1.02095
Subtracted 4.318
1410 serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]
wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] Divided 206.1 210.417 1.02095
1411 polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Subtracted 206.102 210.42 4.318
serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] Divided 1.02095
1412 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] Subtracted 4.318
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] Divided 1.02095

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/