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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Value Type Gene description Rank Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 482 to 531 of 3228 in total
Value Type  : Ranked
Interaction Map  : High confidence
Network Comparison Type  : Divided
Filtered  : 1
description
Rank
red
green
network_comparison
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1910 217.48 215.256 1.01033
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 299 268.635 243.592 1.10281
calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 298 268.632 243.588
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 2181 227.117 225.62 1.00664
calsyntenin-1 precursor. [swissprot;acc:o94985] 2699 188.435 188.31 1.00066
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 2705 188.457 188.334 1.00065
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 2706 188.459 188.336
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1363 218.591 213.899 1.02194
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 0.00001 0.00001 1
camp-dependent protein kinase type i-alpha regulatory chain (tissue- specific extinguisher-1) (tse1). [swissprot;acc:p10644] 3089
camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 2307 215.554 214.467 1.00507
camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 2313 215.529 214.449 1.00504
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 2312 215.542 214.459 1.00505
camp-dependent protein kinase, beta-catalytic subunit (ec 2.7.1.37) (pka c-beta). [swissprot;acc:p22694] 2311
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 2309
candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 1173 229.243 235.246 1.02619
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 1422 203.979 208.229 1.02084
carboxypeptidase a5. [refseq;acc:nm_080385] 1417
carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 1418
carboxypeptidase b precursor. [refseq;acc:nm_020361] 509 177.698 190.239 1.07057
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 717 223.121 211.685 1.05402
carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] 715
carcinoma related gene. [refseq;acc:nm_016041] 3179 0.00001 0.00001 1
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] 1698 217.624 214.69 1.01367
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] 2885 0.00001 0.00001 1
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 226 239.991 269.238 1.12187
casein kinase i alpha s-like. [refseq;acc:nm_145203] 1495 229.459 225.237 1.01874
casein kinase i, alpha isoform (ec 2.7.1.-) (cki-alpha) (ck1). [swissprot;acc:p48729] 1496
casein kinase i, delta isoform (ec 2.7.1.-) (cki-delta) (ckid). [swissprot;acc:p48730] 1721 227.125 224.164 1.01321
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1710 227.225 224.21 1.01345
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 2830 0.00001 0.00001 1
casein kinase i, gamma 2 isoform (ec 2.7.1.-) (cki-gamma 2). [swissprot;acc:p78368] 2986
casein kinase i, gamma 3 isoform (ec 2.7.1.-) (cki-gamma 3). [swissprot;acc:q9y6m4] 2901
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862] 936 232.473 224.372 1.03611
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 863 240.194 230.957 1.03999
casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784] 864
caspase-7 precursor (ec 3.4.22.-) (ice-like apoptotic protease 3) (ice-lap3) (apoptotic protease mch-3) (cmh-1). [swissprot;acc:p55210] 1292 233.942 228.46 1.024
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 1834 180.409 182.459 1.01136
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 1667 214.898 211.898 1.01416
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 1426 214.717 219.157 1.02068
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 1425
caveolin-1. [swissprot;acc:q03135] 3099 0.00001 0.00001 1
caveolin-3 (m-caveolin). [swissprot;acc:p56539] 2779
cbf1 interacting corepressor. [refseq;acc:nm_004882] 572 227.86 213.945 1.06504
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 762 213.256 203.237 1.0493
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 556 207.27 194.368 1.06638
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] 36 260.532 204.309 1.27519
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 408 255.112 234.804 1.08649
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516] 3163 0.00001 0.00001 1
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316] 1390 218.47 213.875 1.02148

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/