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 Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1375 to 1424 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
1375 fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071] FKBP1A 216.542 211.908 1.02187
1376 eyes absent homolog 3. [swissprot;acc:q99504] EYA3 218.537 213.91 1.02163
1377 sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467] SALL2 218.471 213.876 1.02148
1378 sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9] SALL3 218.47
1379 arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102] RERE 213.875
1380 ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818] USP8 213.876
1381 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] ROD1
1382 polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190] PTBP2
1383 adaptor-associated kinase 1. [refseq;acc:nm_014911] AAK1
1384 atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259] ATN1 218.471
1385 dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355] no value 218.47 213.875
1386 rho-gtpase activating protein 10. [refseq;acc:nm_020824] ARHGAP21 213.876
1387 sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2] SALL1 213.875
1388 sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] SALL4 218.471 213.876
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] BCKDHB 218.47 213.875
1390 ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] CNOT4
1391 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] PICALM
1392 clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641] SNAP91 218.471 213.876
1393 membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835] RC3H2 218.47 213.875
1394 polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599] PTBP1
1395 growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861] GAS7 213.876
1396 eyes absent homolog 1. [swissprot;acc:q99502] EYA1 218.463 213.872 1.02147
1397 40s ribosomal protein s8. [swissprot;acc:p09058] RPS8 218.64 214.049 1.02145
1398 eyes absent homolog 4. [swissprot;acc:o95677] EYA4 218.449 213.864 1.02144
1399 eyes absent homolog 2. [swissprot;acc:o00167] EYA2 218.417 213.848 1.02137
1400 cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544] ATF7 218.667 214.118 1.02125
1401 cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336] ATF2 218.657 214.11 1.02124
1402 colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508] MCC 209.682 205.329 1.0212
1403 enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084] ECHS1 184.656 180.823
1404 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] SF3B4 232.752 237.65 1.02104
1405 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] EIF3C 245.532 240.483 1.021
1406 orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] NR6A1 212.833 208.456
1407 wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830] WDFY1 206.104 210.424 1.02096
1408 stromal interaction molecule 1 precursor. [swissprot;acc:q13586] STIM1 206.102 210.42 1.02095
1409 trap/mediator complex component trap25. [refseq;acc:nm_080651] MED30
1410 wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950] WDFY2 206.1 210.417
1411 serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013] PAK4 206.102 210.42
1412 polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765] REEP5
1413 acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310] ACADM
1414 polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393] REEP6
1415 stromal interaction molecule 2 precursor. [swissprot;acc:q9p246] STIM2
1416 serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286] PAK7
1417 carboxypeptidase a5. [refseq;acc:nm_080385] CPA5 203.979 208.229 1.02084
1418 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] CPB1
1419 neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] SLC3A1
1420 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] ACY1
1421 acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] ASAH1 207.076 211.391
1422 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] CPA1 203.979 208.229
1423 cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238] no value 221.152 216.659 1.02074
1424 sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] ATP1A1 214.717 219.157 1.02068

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/