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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Gene Value Type Rank description Filtered Interaction Map Network Comparison Type green red network_comparison
Results: HTML CSV LaTeX Showing element 851 to 900 of 33156 in total
Value Type  : Measured
Filtered  : 1
Network Comparison Type  : Divided
Rank
description
Interaction Map
green
red
network_comparison
426 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] High confidence 6853.15 5942.49 1.15325
proton/amino acid transporter 4. [refseq;acc:nm_152313] Low confidence 9379.02 8913.45 1.05223
427 neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] 8601.49 8174.72 1.05221
trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] High confidence 13531.9 11736.6 1.15297
428 neuronal protein np25. [swissprot;acc:q9ui15] Low confidence 7326.01 6962.59 1.0522
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] High confidence 4288.17 3721.19 1.15237
429 f-box only protein 9. [swissprot;acc:q9uk97] Low confidence 9499.15 9028.53 1.05213
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] High confidence 7226.06 6272.91 1.15195
430 sortilin precursor (glycoprotein 95) (gp95) (neurotensin receptor 3) (nt3) (100 kda nt receptor). [swissprot;acc:q99523] Low confidence 8777.22 8342.99 1.05205
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] High confidence 4379.37 3804.09 1.15123
431 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 4431.36 3849.94 1.15102
high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083] Low confidence 9368.48 8906.4 1.05188
432 mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] High confidence 6036.27 5244.71 1.15093
solute carrier family 36 member 1; proton / amino acid symporter; lysosomal amino acid transporter 1. [refseq;acc:nm_078483] Low confidence 9368.48 8906.4 1.05188
433 mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] High confidence 6036.38 5244.88 1.15091
transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802] Low confidence 7345.76 6983.46 1.05188
434 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 8276.86 7870.63 1.05161
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] High confidence 6037.37 5246.38 1.15077
435 cytochrome p450 51a1 (ec 1.14.13.70) (cypli) (p450li) (sterol 14-alpha demethylase) (lanosterol 14-alpha demethylase) (ldm) (p450-14dm). [swissprot;acc:q16850] Low confidence 8139.75 7740.82 1.05154
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] High confidence 6022.6 5233.86 1.1507
436 arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] 7168.2 6230.94 1.15042
brain protein 16. [refseq;acc:nm_016458] Low confidence 9277.39 8822.87 1.05152
437 proactivator polypeptide precursor [contains: saposin a (protein a); saposin b (sphingolipid activator protein 1) (sap-1) (cerebroside sulfate activator) (csact) (dispersin) (sulfatide/gm1 activator); saposin c (co-beta-glucosidase) (a1 activator) (glucosylceramidase activator) (sphingolipid activator protein 2) (sap-2); saposin d (protein c) (component c)]. [swissprot;acc:p07602] 8190.1 7789.85 1.05138
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] High confidence 4348.48 3779.92 1.15042
438 sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538] Low confidence 7981.63 7591.67 1.05137
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] High confidence 7192.88 6252.58 1.15039
439 ectonucleoside triphosphate diphosphohydrolase 6 (ec 3.6.1.6) (ntpdase6) (cd39 antigen-like 2). [swissprot;acc:o75354] Low confidence 9342.85 8886.95 1.0513
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] High confidence 7192.88 6252.58 1.15039
440 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 7192.08 6251.91 1.15038
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Low confidence 6694.68 6368.6 1.0512
441 grancalcin. [swissprot;acc:p28676] High confidence 7192.13 6251.96 1.15038
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Low confidence 8185.37 7787.16 1.05114
442 p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44] 9458.43 8998.58 1.0511
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] High confidence 7192.17 6251.99 1.15038
443 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 7192.51 6252.27
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Low confidence 8229.98 7831.81 1.05084
444 nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573] 9072.08 8633.61 1.05079
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] High confidence 4322.87 3758.67 1.15011
445 ad24 protein. [refseq;acc:nm_022451] 4315.95 3753.71 1.14978
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Low confidence 6723.57 6398.89 1.05074
446 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 6724.31 6399.67 1.05073
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] High confidence 4329.37 3766.03 1.14958
447 o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Low confidence 9347.66 8896.45 1.05072
pescadillo homolog 1. [swissprot;acc:o00541] High confidence 4310.89 3751.14 1.14922
448 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 7190.91 6259.3 1.14884
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Low confidence 9360.97 8909.72 1.05065
449 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 8179.81 7786.29 1.05054
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] High confidence 4319.69 3761.59 1.14837
450 aquaporin 6 (aquaporin-2 like) (hkid). [swissprot;acc:q13520] Low confidence 9305.48 8858.26 1.05049
l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] High confidence 5610.52 4889.21 1.14753

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/