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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Gene Rank Value Type Network Comparison Type description Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 551 to 600 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
description
green
red
network_comparison
276 Divided 60s ribosomal protein l32. [swissprot;acc:p02433] 266.969 241.13 1.10716
Subtracted atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 235.183 258.437 23.254
277 Divided 40s ribosomal protein s29. [swissprot;acc:p30054] 267.642 241.849 1.10665
Subtracted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 262.434 239.277 23.157
278 Divided 40s ribosomal protein s11. [swissprot;acc:p04643] 267.088 241.399 1.10642
Subtracted myelin gene expression factor 2. [refseq;acc:nm_016132] 258.476 235.383 23.093
279 Divided 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
Subtracted trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 265.715 242.66 23.055
280 Divided metastasis-associated protein mta1. [swissprot;acc:q13330] 228.356 252.512 1.10578
Subtracted transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 244.168 267.208 23.04
281 Divided 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 267.335 241.808 1.10557
Subtracted 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 265.104 242.159 22.945
282 Divided 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
Subtracted nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] 265.104 242.159 22.945
283 Divided 60s ribosomal protein l11. [swissprot;acc:p39026] 267.346 241.828 1.10552
Subtracted 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 265.255 242.37 22.885
284 Divided crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 203.235 224.657 1.10541
Subtracted dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 265.516 242.686 22.83
285 Divided 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
Subtracted dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 265.481 242.691 22.79
286 Divided 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
Subtracted 60s ribosomal protein l30. [swissprot;acc:p04645] 265.365 242.593 22.772
287 Divided 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 266.079 240.758 1.10517
Subtracted splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] 202.459 225.217 22.758
288 Divided 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 266.078 240.758 1.10517
Subtracted syntaxin 10 (syn10). [swissprot;acc:o60499] 257.442 234.691 22.751
289 Divided hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 246.892 272.781 1.10486
Subtracted syntaxin 6. [swissprot;acc:o43752] 257.414 234.673 22.741
290 Divided ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 210.064 231.969 1.10428
Subtracted suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 264.79 242.109 22.681
291 Divided 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
Subtracted adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 264.163 241.509 22.654
292 Divided 40s ribosomal protein s15a. [swissprot;acc:p39027] 266.414 241.411 1.10357
Subtracted heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] 256.627 234.146 22.481
293 Divided 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 265.717 240.782 1.10356
Subtracted c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 196.978 219.421 22.443
294 Divided 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
Subtracted heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 196.978 219.421 22.443
295 Divided 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
Subtracted heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 196.978 219.421 22.443
296 Divided mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 266.12 241.282 1.10294
Subtracted heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 196.978 219.421 22.443
297 Divided 60s ribosomal protein l7. [swissprot;acc:p18124] 259.984 235.727 1.1029
Subtracted mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 196.978 219.421 22.443
298 Divided 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
Subtracted 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] 244.236 266.421 22.185
299 Divided 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
Subtracted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 244.236 266.421 22.185
300 Divided metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 166.351 150.959 1.10196
Subtracted probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 234.945 257.017 22.072

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/