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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Filtered Gene Rank Network Comparison Type description Value Type Interaction Map green network_comparison red
Results: HTML CSV LaTeX Showing element 551 to 600 of 8289 in total
Filtered  : 1
Network Comparison Type  : Divided
Value Type  : Ranked
Rank
description
Interaction Map
green
network_comparison
red
276 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Low confidence 191.474 1.04421 199.939
60s ribosomal protein l32. [swissprot;acc:p02433] High confidence 266.969 1.10716 241.13
277 40s ribosomal protein s29. [swissprot;acc:p30054] 267.642 1.10665 241.849
cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] Low confidence 202.965 1.04408 211.912
278 40s ribosomal protein s11. [swissprot;acc:p04643] High confidence 267.088 1.10642 241.399
asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82] Low confidence 196.369 1.04398 205.006
279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] High confidence 228.42 1.10605 252.644
transcriptional repressor nac1. [refseq;acc:nm_052876] Low confidence 211.2 1.04395 202.309
280 lbp-9. [refseq;acc:nm_014553] 210.509 1.04394 219.758
metastasis-associated protein mta1. [swissprot;acc:q13330] High confidence 228.356 1.10578 252.512
281 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 267.335 1.10557 241.808
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Low confidence 210.503 1.04392 219.749
282 alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745] 210.498 1.04391 219.742
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 228.297 1.10553 252.39
283 60s ribosomal protein l11. [swissprot;acc:p39026] 267.346 1.10552 241.828
upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517] Low confidence 210.484 1.04389 219.722
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] High confidence 203.235 1.10541 224.657
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 205.692 1.04367 214.675
285 t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] High confidence 203.242 1.10532 224.647
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Low confidence 211.175 1.04359 202.354
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 203.251 1.1052 224.633
transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750] Low confidence 211.174 1.04358 202.356
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] High confidence 266.079 1.10517 240.758
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 201.397 1.04337 210.132
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] High confidence 266.078 1.10517 240.758
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Low confidence 192.004 1.04314 200.288
289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] High confidence 246.892 1.10486 272.781
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Low confidence 200.66 1.04311 209.31
290 lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407] 201.325 1.04309 210
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] High confidence 210.064 1.10428 231.969
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] 228.037 1.10368 251.679
pl6 protein (placental protein 6). [swissprot;acc:q12893] Low confidence 201.322 1.04308 209.995
292 40s ribosomal protein s15a. [swissprot;acc:p39027] High confidence 266.414 1.10357 241.411
lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012] Low confidence 201.322 1.04308 209.995
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] High confidence 265.717 1.10356 240.782
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] Low confidence 209.763 1.04301 218.785
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 265.717 1.10356 240.782
jagged 2 precursor (jagged2) (hj2). [swissprot;acc:q9y219] Low confidence 209.71 1.04294 218.715
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 202.423 1.103 223.273
myocyte-specific enhancer factor 2d. [swissprot;acc:q14814] Low confidence 209.709 1.04294 218.713
296 jagged 1 precursor (jagged1) (hj1). [swissprot;acc:p78504] 218.714
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] High confidence 266.12 1.10294 241.282
297 60s ribosomal protein l7. [swissprot;acc:p18124] 259.984 1.1029 235.727
myocyte-specific enhancer factor 2c. [swissprot;acc:q06413] Low confidence 209.709 1.04294 218.714
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 243.588 1.10281 268.632
myocyte-specific enhancer factor 2a (serum response factor-like protein 1). [swissprot;acc:q02078] Low confidence 209.71 1.04294 218.715
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 243.592 1.10281 268.635
endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [swissprot;acc:q9upy3] Low confidence 200.322 1.0429 208.915
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] 209.669 1.04289 218.661
metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] High confidence 166.351 1.10196 150.959

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/