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 975 to 1024 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
488 gaba-a receptor-associated protein. [sptrembl;acc:q9by60] Subtracted 82.5916 98.0548 15.4632
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Divided 225.026 209.798 1.07258
489 apg3p; pc3-96 protein. [refseq;acc:nm_022488] Subtracted 82.5916 98.0548 15.4632
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Divided 231.276 215.627 1.07257
490 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Subtracted 242.531 227.136 15.395
rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155] Divided 220.183 236.015 1.0719
491 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Subtracted 150.959 166.351 15.392
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Divided 251.83 234.951 1.07184
492 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Subtracted 150.982 166.372 15.39
serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177] Divided 220.171 235.979 1.0718
493 conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83] 220.172 235.98
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Subtracted 236.751 252.038 15.287
494 metaxin 2. [swissprot;acc:o75431] 219.537 234.793 15.256
serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153] Divided 220.172 235.98 1.0718
495 serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914] 220.171 235.979
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Subtracted 222.146 237.393 15.247
496 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 235.18 250.419 15.239
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Divided 250.938 234.134 1.07177
497 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 251.344 234.514
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Subtracted 225.026 209.798 15.228
498 rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052] Divided 220.161 235.95 1.07172
t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] Subtracted 237.28 252.492 15.212
499 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Divided 231.496 248.048 1.0715
500 inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564] 224.662 240.673 1.07127
opsin 4 (melanopsin). [swissprot;acc:q9uhm6] Subtracted 237.28 252.492 15.212
501 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Divided 238.704 255.68 1.07112
t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763] Subtracted 237.28 252.492 15.212
502 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Divided 238.704 255.68 1.07112
t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314] Subtracted 237.28 252.492 15.212
503 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Divided 238.704 255.68 1.07112
504 homeobox protein barh-like 2. [swissprot;acc:q9umq3] Subtracted 237.28 252.492 15.212
oligophrenin 1. [swissprot;acc:o60890] Divided 238.704 255.68 1.07112
505 ad24 protein. [refseq;acc:nm_022451] 251.334 234.672 1.071
zinc finger protein t86. [swissprot;acc:o00488] Subtracted 246.805 231.796 15.009
506 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 215.237 230.07 14.833
inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537] Divided 224.535 240.476 1.071
507 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Subtracted 215.237 230.07 14.833
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Divided 251.299 234.729 1.07059
508 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 177.698 190.24 1.07058
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Subtracted 228.255 213.422 14.833
509 carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 177.698 190.239 1.07057
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Subtracted 215.237 230.07 14.833
510 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Divided 177.699 190.24 1.07057
511 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] 250.053 233.725 1.06986
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Subtracted 214.754 229.565 14.811
512 block of proliferation 1. [swissprot;acc:q14137] Divided 250.794 234.433 1.06979
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Subtracted 229.803 215.301 14.502

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/