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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1432 to 1481 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
358 serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Rooted 61.2684 67.755 1.10587
359 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Ranked 239.277 262.434 1.09678
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured 12798.9 10887.2 1.17559
pescadillo homolog 1. [swissprot;acc:o00541] Rooted 49.2488 54.4603 1.10582
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Squared 9812.34 7908.87 1.24068
360 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured 12796.8 10886 1.17553
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Rooted 49.3771 54.5905 1.10558
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 266.559 1.09663
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Squared 9814.47 7911.48 1.24054
361 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Rooted 50.7801 45.9472 1.10518
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Measured 12787.6 10880.5 1.17528
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Ranked 242.83 266.248 1.09644
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Squared 70694.1 56989.9 1.24047
362 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Rooted 50.7803 45.9477 1.10518
apical-like protein (apxl protein). [swissprot;acc:q13796] Ranked 231.492 211.136 1.09641
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Measured 12786.6 10879.9 1.17525
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Squared 57808.9 46630.3 1.23973
363 block of proliferation 1. [swissprot;acc:q14137] Rooted 49.4884 54.6735 1.10477
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Measured 12780.7 10876.4 1.17509
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Ranked 231.481 211.131 1.09639
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Squared 57579.2 46497.2 1.23834
364 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Rooted 50.0785 55.3215 1.1047
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Ranked 243.208 266.617 1.09625
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Measured 5189 6088.47 1.17334
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Squared 17957.2 22234.1 1.23817
365 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked 242.744 266.07 1.09609
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Squared 17965.8 22243 1.23807
calcyphosine. [swissprot;acc:q13938] Measured 5189 6088.47 1.17334
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted 49.7541 54.9425 1.10428
366 40s ribosomal protein s15a. [swissprot;acc:p39027] 50.5463 45.7763 1.1042
40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 242.473 265.756 1.09602
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared 62783.5 50784.1 1.23628
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 5189 6088.47 1.17334
367 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Rooted 49.0882 54.2027 1.10419
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared 62757.7 50767.8 1.23617
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured 4024.4 4719.35 1.17268
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 234.146 256.627 1.09601
368 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared 51805.2 41916.4 1.23592
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Rooted 49.5225 54.6817 1.10418
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Measured 5082.66 5959.99 1.17261
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked 242.66 265.715 1.09501
369 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 1.09475
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Measured 3583.56 4194.95 1.17061
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Squared 45960.8 56749.6 1.23474
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Rooted 49.7435 45.0586 1.10397
370 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Measured 4108.15 4808.93 1.17058
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] Rooted 49.7435 45.0586 1.10397
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Ranked 242.159 265.104 1.09475
protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Squared 45986 56776.1 1.23464
371 band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0] 45985.9 56776

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/