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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Rank Gene description Hugo Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 313 to 362 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
red
green
network_comparison
313 ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] RRM2B 232.473 211.207 1.10069
314 methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] METAP1 244.126 268.604 1.10027
315 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] METAP2
316 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] EIF1 242.694 267.017 1.10022
317 splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] no value 224.445 204.044 1.09998
318 mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] MRPL3 242.011 266.18 1.09987
319 60s ribosomal protein l19. [swissprot;acc:p14118] RPL19 240.73 264.729 1.09969
320 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] CDH1 241.892 265.96 1.0995
321 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] no value 265.959 1.09949
322 deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] DNASE2B 86.7483 78.8995 1.09948
323 60s ribosomal protein l23a. [swissprot;acc:p29316] no value 241.884 265.945 1.09947
324 40s ribosomal protein s23. [swissprot;acc:p39028] RPS23 243.944 268.195 1.09941
325 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] MRPS12
326 60s ribosomal protein l5. [swissprot;acc:p46777] RPL5 241.899 265.924 1.09932
327 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] POLR2A 243.817 267.962 1.09903
328 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] DDX24 258.437 235.183 1.09888
329 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 312 284 1.09859
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] CHD3
331 doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2
332 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6
333 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1
334 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] NEUROD4
335 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] CHD5
336 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] CDK2AP1
337 60s ribosomal protein l12. [swissprot;acc:p30050] no value 243.583 267.527 1.0983
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 267.528
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 267.527
340 myelin gene expression factor 2. [refseq;acc:nm_016132] MYEF2 235.383 258.476 1.09811
341 60s ribosomal protein l9. [swissprot;acc:p32969] no value 240.243 263.798 1.09805
342 40s ribosomal protein s20. [swissprot;acc:p17075] RPS20 243.5 267.21 1.09737
343 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] PRMT3 241.625 265.136 1.0973
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] no value
345 ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] CMPK 242.14 265.697 1.09729
346 40s ribosomal protein s3. [swissprot;acc:p23396] RPS3 241.612 265.119
347 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] AK3 242.14 265.697
348 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] no value 265.696 1.09728
349 surfeit locus protein 5. [swissprot;acc:q15528] MED22
350 zinc finger protein 291. [swissprot;acc:q9by12] SCAPER
351 peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] PEX1
352 protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] TXNDC9
353 rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] GIPC1 231.73 211.252 1.09694
354 syntaxin 10 (syn10). [swissprot;acc:o60499] STX10 234.691 257.442
355 syntaxin 6. [swissprot;acc:o43752] STX6 234.673 257.414 1.09691
356 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] no value 243.24 266.796 1.09684
357 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 243.12 266.661 1.09683
358 ribosomal protein l10-like protein. [refseq;acc:nm_080746] RPL10L 266.662
359 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] RPL4 239.277 262.434 1.09678
360 protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] SEC61G 243.072 266.559 1.09663
361 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] MRPL17 242.83 266.248 1.09644
362 apical-like protein (apxl protein). [swissprot;acc:q13796] SHROOM2 231.492 211.136 1.09641

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
- Hugo is the HGNC identifier if it exists
- 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/