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 Network Comparison Type Value Type Rank description green Interaction Map Filtered red network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 7460 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
green
Filtered
red
network_comparison
276 60s ribosomal protein l32. [swissprot;acc:p02433] 266.969 1 241.13 1.10716
60s ribosomal protein l9. [swissprot;acc:p32969] 9922.33 0 10741.6 1.08257
277 40s ribosomal protein s29. [swissprot;acc:p30054] 267.642 1 241.849 1.10665
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 10251.6 0 11096.8 1.08245
278 40s ribosomal protein s11. [swissprot;acc:p04643] 267.088 1 241.399 1.10642
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 10763.4 0 11644 1.08181
279 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 9812.39 10614.2 1.08171
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 228.42 1 252.644 1.10605
280 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 11471.2 0 10620.1 1.08014
metastasis-associated protein mta1. [swissprot;acc:q13330] 228.356 1 252.512 1.10578
281 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 267.335 241.808 1.10557
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 13514.5 0 12522.7 1.0792
282 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 228.297 1 252.39 1.10553
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] 8732.68 0 8095.69 1.07868
283 60s ribosomal protein l11. [swissprot;acc:p39026] 267.346 1 241.828 1.10552
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 11959.2 0 11107.1 1.07672
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 203.235 1 224.657 1.10541
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 16041.6 0 14898.9 1.0767
285 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 9925.58 10686 1.07661
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 203.242 1 224.647 1.10532
286 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 11367.3 0 12228.2 1.07573
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 203.251 1 224.633 1.1052
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 266.079 240.758 1.10517
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 16590.3 0 17842.7 1.07549
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 266.078 1 240.758 1.10517
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 16053 0 14930.6 1.07517
289 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 14091.9 15147.2 1.07489
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 246.892 1 272.781 1.10486
290 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 14091.9 0 15147.2 1.07489
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 210.064 1 231.969 1.10428
291 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 11731.8 0 10922.9 1.07406
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] 228.037 1 251.679 1.10368
292 40s ribosomal protein s15a. [swissprot;acc:p39027] 266.414 241.411 1.10357
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 9574.98 0 10280.5 1.07368
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 265.717 1 240.782 1.10356
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 9583.27 0 10287.1 1.07344
294 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] 265.717 1 240.782 1.10356
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 13025.1 0 13981.5 1.07343
295 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 202.423 1 223.273 1.103
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 12751.8 0 13687.7 1.07339
296 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 10941.8 10194.1 1.07335
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 266.12 1 241.282 1.10294
297 60s ribosomal protein l7. [swissprot;acc:p18124] 259.984 235.727 1.1029
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 8719 0 8123.75 1.07327
298 40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865] 12842.5 11977.8 1.07219
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] 243.588 1 268.632 1.10281
299 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 11512.3 0 12338.7 1.07178
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 243.592 1 268.635 1.10281
300 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 8650.24 0 9270.49 1.0717
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 166.351 1 150.959 1.10196

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/