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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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