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 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
276 60s ribosomal protein l32. [swissprot;acc:p02433] Divided 241.13 1.10716 266.969
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Subtracted 258.437 23.254 235.183
277 40s ribosomal protein s29. [swissprot;acc:p30054] Divided 241.849 1.10665 267.642
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 239.277 23.157 262.434
278 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 241.399 1.10642 267.088
myelin gene expression factor 2. [refseq;acc:nm_016132] Subtracted 235.383 23.093 258.476
279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 252.644 1.10605 228.42
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Subtracted 242.66 23.055 265.715
280 metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 252.512 1.10578 228.356
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted 267.208 23.04 244.168
281 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 22.945 265.104
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 241.808 1.10557 267.335
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] 252.39 1.10553 228.297
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Subtracted 242.159 22.945 265.104
283 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 22.885 265.255
60s ribosomal protein l11. [swissprot;acc:p39026] Divided 241.828 1.10552 267.346
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 1.10541 203.235
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Subtracted 242.686 22.83 265.516
285 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 242.691 22.79 265.481
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Divided 224.647 1.10532 203.242
286 60s ribosomal protein l30. [swissprot;acc:p04645] Subtracted 242.593 22.772 265.365
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] Divided 224.633 1.1052 203.251
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 1.10517 266.079
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted 225.217 22.758 202.459
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Divided 240.758 1.10517 266.078
syntaxin 10 (syn10). [swissprot;acc:o60499] Subtracted 234.691 22.751 257.442
289 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Divided 272.781 1.10486 246.892
syntaxin 6. [swissprot;acc:o43752] Subtracted 234.673 22.741 257.414
290 ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] Divided 231.969 1.10428 210.064
suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] Subtracted 242.109 22.681 264.79
291 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 241.509 22.654 264.163
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] Divided 251.679 1.10368 228.037
292 40s ribosomal protein s15a. [swissprot;acc:p39027] 241.411 1.10357 266.414
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Subtracted 234.146 22.481 256.627
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Divided 240.782 1.10356 265.717
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Subtracted 219.421 22.443 196.978
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] Divided 240.782 1.10356 265.717
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Subtracted 219.421 22.443 196.978
295 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Divided 223.273 1.103 202.423
296 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Subtracted 219.421 22.443 196.978
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Divided 241.282 1.10294 266.12
297 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 1.1029 259.984
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Subtracted 219.421 22.443 196.978
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] Divided 268.632 1.10281 243.588
transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094] Subtracted 266.421 22.185 244.236
299 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Divided 268.635 1.10281 243.592
transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] Subtracted 266.421 22.185 244.236
300 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Divided 150.959 1.10196 166.351
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Subtracted 257.017 22.072 234.945

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/