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 Value Type Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 551 to 600 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
network_comparison
green
276 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Low confidence 199.939 1.04421 191.474
60s ribosomal protein l32. [swissprot;acc:p02433] High confidence 241.13 1.10716 266.969
277 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 1.10665 267.642
cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 211.912 1.04408 202.965
278 40s ribosomal protein s11. [swissprot;acc:p04643] High confidence 241.399 1.10642 267.088
asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82] Low confidence 205.006 1.04398 196.369
279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] High confidence 252.644 1.10605 228.42
transcriptional repressor nac1. [refseq;acc:nm_052876] Low confidence 202.309 1.04395 211.2
280 lbp-9. [refseq;acc:nm_014553] 219.758 1.04394 210.509
metastasis-associated protein mta1. [swissprot;acc:q13330] High confidence 252.512 1.10578 228.356
281 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 1.10557 267.335
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Low confidence 219.749 1.04392 210.503
282 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 219.742 1.04391 210.498
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] High confidence 252.39 1.10553 228.297
283 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 1.10552 267.346
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Low confidence 219.722 1.04389 210.484
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence 224.657 1.10541 203.235
tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2] Low confidence 214.675 1.04367 205.692
285 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 224.647 1.10532 203.242
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Low confidence 202.354 1.04359 211.175
286 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] High confidence 224.633 1.1052 203.251
transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] Low confidence 202.356 1.04358 211.174
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 240.758 1.10517 266.079
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Low confidence 210.132 1.04337 201.397
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] High confidence 240.758 1.10517 266.078
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Low confidence 200.288 1.04314 192.004
289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] High confidence 272.781 1.10486 246.892
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Low confidence 209.31 1.04311 200.66
290 lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] 210 1.04309 201.325
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] High confidence 231.969 1.10428 210.064
291 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
pl6 protein (placental protein 6). [swissprot;acc:q12893] Low confidence 209.995 1.04308 201.322
292 40s ribosomal protein s15a. [swissprot;acc:p39027] High confidence 241.411 1.10357 266.414
lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Low confidence 209.995 1.04308 201.322
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] High confidence 240.782 1.10356 265.717
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence 218.785 1.04301 209.763
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] High confidence 240.782 1.10356 265.717
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Low confidence 218.715 1.04294 209.71
295 multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] High confidence 223.273 1.103 202.423
myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Low confidence 218.713 1.04294 209.709
296 jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] 218.714
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] High confidence 241.282 1.10294 266.12
297 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 1.1029 259.984
myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence 218.714 1.04294 209.709
298 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] High confidence 268.632 1.10281 243.588
myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Low confidence 218.715 1.04294 209.71
299 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] High confidence 268.635 1.10281 243.592
endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [swissprot;acc:q9upy3] Low confidence 208.915 1.0429 200.322
300 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] 218.661 1.04289 209.669
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] High confidence 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/