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

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/