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.


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

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/