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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank Value Type Network Comparison Type description Interaction Map Filtered red green 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
red
green
network_comparison
276 Divided 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 266.969 1.10716
Subtracted atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 258.437 235.183 23.254
277 Divided 40s ribosomal protein s29. [swissprot;acc:p30054] 241.849 267.642 1.10665
Subtracted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 239.277 262.434 23.157
278 Divided 40s ribosomal protein s11. [swissprot;acc:p04643] 241.399 267.088 1.10642
Subtracted myelin gene expression factor 2. [refseq;acc:nm_016132] 235.383 258.476 23.093
279 Divided histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 252.644 228.42 1.10605
Subtracted trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 242.66 265.715 23.055
280 Divided metastasis-associated protein mta1. [swissprot;acc:q13330] 252.512 228.356 1.10578
Subtracted transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] 267.208 244.168 23.04
281 Divided 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 241.808 267.335 1.10557
Subtracted 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 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] 252.39 228.297 1.10553
Subtracted nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] 242.159 265.104 22.945
283 Divided 60s ribosomal protein l11. [swissprot;acc:p39026] 241.828 267.346 1.10552
Subtracted 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 265.255 22.885
284 Divided crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 224.657 203.235 1.10541
Subtracted dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] 242.686 265.516 22.83
285 Divided t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 224.647 203.242 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] 242.691 265.481 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] 224.633 203.251 1.1052
Subtracted 60s ribosomal protein l30. [swissprot;acc:p04645] 242.593 265.365 22.772
287 Divided 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 266.079 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] 225.217 202.459 22.758
288 Divided 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] 240.758 266.078 1.10517
Subtracted syntaxin 10 (syn10). [swissprot;acc:o60499] 234.691 257.442 22.751
289 Divided hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 272.781 246.892 1.10486
Subtracted syntaxin 6. [swissprot;acc:o43752] 234.673 257.414 22.741
290 Divided ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 231.969 210.064 1.10428
Subtracted suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169] 242.109 264.79 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] 251.679 228.037 1.10368
Subtracted adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 241.509 264.163 22.654
292 Divided 40s ribosomal protein s15a. [swissprot;acc:p39027] 241.411 266.414 1.10357
Subtracted heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] 234.146 256.627 22.481
293 Divided 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] 240.782 265.717 1.10356
Subtracted c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 219.421 196.978 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] 240.782 265.717 1.10356
Subtracted heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] 219.421 196.978 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] 223.273 202.423 1.103
Subtracted heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] 219.421 196.978 22.443
296 Divided mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] 241.282 266.12 1.10294
Subtracted heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] 219.421 196.978 22.443
297 Divided 60s ribosomal protein l7. [swissprot;acc:p18124] 235.727 259.984 1.1029
Subtracted mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] 219.421 196.978 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] 268.632 243.588 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] 266.421 244.236 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] 268.635 243.592 1.10281
Subtracted transcription factor e2f2 (e2f-2). [swissprot;acc:q14209] 266.421 244.236 22.185
300 Divided metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 150.959 166.351 1.10196
Subtracted probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 257.017 234.945 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/