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 Network Comparison Type Gene description Rank Filtered Interaction Map network_comparison green red
Results: HTML CSV LaTeX Showing element 480 to 529 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
description
Rank
network_comparison
green
red
calmegin precursor. [swissprot;acc:o14967] 1909 1.01033 215.256 217.48
calmodulin. [swissprot;acc:p02593] 2928 1 0.00001 0.00001
calnexin precursor (major histocompatibility complex class i antigen-binding protein p88) (p90) (ip90). [swissprot;acc:p27824] 1910 1.01033 215.256 217.48
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 299 1.10281 243.592 268.635
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] 298 243.588 268.632
calreticulin precursor (crp55) (calregulin) (hacbp) (erp60). [swissprot;acc:p27797] 2181 1.00664 225.62 227.117
calsyntenin-1 precursor. [swissprot;acc:o94985] 2699 1.00066 188.31 188.435
calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 2705 1.00065 188.334 188.457
calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 2706 188.336 188.459
camp response element-binding protein cre-bpa. [refseq;acc:nm_004904] 1363 1.02194 213.899 218.591
camp responsive element binding protein-like 2. [refseq;acc:nm_001310] 3078 1 0.00001 0.00001
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 1.00507 214.467 215.554
camp-dependent protein kinase type ii-beta regulatory chain. [swissprot;acc:p31323] 2313 1.00504 214.449 215.529
camp-dependent protein kinase, alpha-catalytic subunit (ec 2.7.1.37) (pka c-alpha). [swissprot;acc:p17612] 2312 1.00505 214.459 215.542
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 1.02619 235.246 229.243
carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 1422 1.02084 208.229 203.979
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 1.07057 190.239 177.698
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 717 1.05402 211.685 223.121
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 1 0.00001 0.00001
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] 1698 1.01367 214.69 217.624
carnitine o-palmitoyltransferase ii, mitochondrial precursor (ec 2.3.1.21) (cpt ii). [swissprot;acc:p23786] 2885 1 0.00001 0.00001
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 226 1.12187 269.238 239.991
casein kinase i alpha s-like. [refseq;acc:nm_145203] 1495 1.01874 225.237 229.459
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 1.01321 224.164 227.125
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] 1710 1.01345 224.21 227.225
casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0] 2830 1 0.00001 0.00001
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 1.03611 224.372 232.473
casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 863 1.03999 230.957 240.194
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 1.024 228.46 233.942
catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 1834 1.01136 182.459 180.409
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] 1667 1.01416 211.898 214.898
cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711] 1426 1.02068 219.157 214.717
cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 1425
caveolin-1. [swissprot;acc:q03135] 3099 1 0.00001 0.00001
caveolin-3 (m-caveolin). [swissprot;acc:p56539] 2779
cbf1 interacting corepressor. [refseq;acc:nm_004882] 572 1.06504 213.945 227.86
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 762 1.0493 203.237 213.256
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] 556 1.06638 194.368 207.27
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 1.27519 204.309 260.532
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] 408 1.08649 234.804 255.112

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/