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 Network Comparison Type Value Type Interaction Map green red network_comparison Filtered
Results: HTML CSV LaTeX Showing element 551 to 600 of 3730 in total
Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
green
red
network_comparison
Filtered
276 60s ribosomal protein l32. [swissprot;acc:p02433] 266.969 241.13 1.10716 1
60s ribosomal protein l9. [swissprot;acc:p32969] 9922.33 10741.6 1.08257 0
277 40s ribosomal protein s29. [swissprot;acc:p30054] 267.642 241.849 1.10665 1
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 10251.6 11096.8 1.08245 0
278 40s ribosomal protein s11. [swissprot;acc:p04643] 267.088 241.399 1.10642 1
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 10763.4 11644 1.08181 0
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] 228.42 252.644 1.10605 1
280 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 11471.2 10620.1 1.08014 0
metastasis-associated protein mta1. [swissprot;acc:q13330] 228.356 252.512 1.10578 1
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 12522.7 1.0792 0
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] 228.297 252.39 1.10553 1
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 8095.69 1.07868 0
283 60s ribosomal protein l11. [swissprot;acc:p39026] 267.346 241.828 1.10552 1
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 11959.2 11107.1 1.07672 0
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 203.235 224.657 1.10541 1
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 16041.6 14898.9 1.0767 0
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] 203.242 224.647 1.10532 1
286 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 11367.3 12228.2 1.07573 0
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] 203.251 224.633 1.1052 1
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 17842.7 1.07549 0
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 266.078 240.758 1.10517 1
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 14930.6 1.07517 0
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] 246.892 272.781 1.10486 1
290 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 14091.9 15147.2 1.07489 0
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 210.064 231.969 1.10428 1
291 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 11731.8 10922.9 1.07406 0
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] 228.037 251.679 1.10368 1
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 10280.5 1.07368 0
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 265.717 240.782 1.10356 1
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 10287.1 1.07344 0
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] 265.717 240.782 1.10356 1
transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 13025.1 13981.5 1.07343 0
295 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 202.423 223.273 1.103 1
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 12751.8 13687.7 1.07339 0
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] 266.12 241.282 1.10294 1
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 8123.75 1.07327 0
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] 243.588 268.632 1.10281 1
299 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 11512.3 12338.7 1.07178 0
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 243.592 268.635 1.10281 1
300 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 8650.24 9270.49 1.0717 0
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 166.351 150.959 1.10196 1

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/