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 Filtered description Value Type Network Comparison Type Interaction Map red network_comparison green
Results: HTML CSV LaTeX Showing element 551 to 600 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Filtered
description
red
network_comparison
green
276 0 60s ribosomal protein l9. [swissprot;acc:p32969] 10741.6 1.08257 9922.33
1 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 1.10716 266.969
277 0 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 11096.8 1.08245 10251.6
1 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 1.10665 267.642
278 0 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 11644 1.08181 10763.4
1 40s ribosomal protein s11. [swissprot;acc:p04643] 241.399 1.10642 267.088
279 0 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 10614.2 1.08171 9812.39
1 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 1.10605 228.42
280 0 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] 10620.1 1.08014 11471.2
1 metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 1.10578 228.356
281 0 phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] 12522.7 1.0792 13514.5
1 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 1.10557 267.335
282 0 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] 8095.69 1.07868 8732.68
1 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] 252.39 1.10553 228.297
283 0 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 11107.1 1.07672 11959.2
1 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 1.10552 267.346
284 0 tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] 14898.9 1.0767 16041.6
1 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 1.10541 203.235
285 0 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 10686 1.07661 9925.58
1 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 224.647 1.10532 203.242
286 0 dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] 12228.2 1.07573 11367.3
1 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] 224.633 1.1052 203.251
287 0 proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] 17842.7 1.07549 16590.3
1 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 1.10517 266.079
288 0 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] 14930.6 1.07517 16053
1 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 1.10517 266.078
289 0 forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] 15147.2 1.07489 14091.9
1 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 1.10486 246.892
290 0 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] 15147.2 1.07489 14091.9
1 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 231.969 1.10428 210.064
291 0 far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] 10922.9 1.07406 11731.8
1 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] 251.679 1.10368 228.037
292 0 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 10280.5 1.07368 9574.98
1 40s ribosomal protein s15a. [swissprot;acc:p39027] 241.411 1.10357 266.414
293 0 ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] 10287.1 1.07344 9583.27
1 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 1.10356 265.717
294 0 transcription initiation factor tfiid 20/15 kda subunits (tafii- 20/tafii-15) (tafii20/tafii15). [swissprot;acc:q16514] 13981.5 1.07343 13025.1
1 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] 240.782 1.10356 265.717
295 0 transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] 13687.7 1.07339 12751.8
1 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] 223.273 1.103 202.423
296 0 lon protease homolog, mitochondrial precursor (ec 3.4.21.-) (lon protease-like protein) (lonp) (lonhs). [swissprot;acc:p36776] 10194.1 1.07335 10941.8
1 mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 241.282 1.10294 266.12
297 0 daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959] 8123.75 1.07327 8719
1 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 1.1029 259.984
298 0 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] 11977.8 1.07219 12842.5
1 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] 268.632 1.10281 243.588
299 0 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 12338.7 1.07178 11512.3
1 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 268.635 1.10281 243.592
300 0 camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] 9270.49 1.0717 8650.24
1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 150.959 1.10196 166.351

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/