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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1428 to 1477 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
357 PPP2R2D uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Squared 9811.86 7908.29 1.24071
358 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Measured 5061.11 5950.22 1.17567
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Squared 9811.73 7908.13 1.24071
NEK2 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
RPL10L ribosomal protein l10-like protein. [refseq;acc:nm_080746] Ranked 243.12 266.662 1.09683
359 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured 12798.9 10887.2 1.17559
PES1 pescadillo homolog 1. [swissprot;acc:o00541] Rooted 49.2488 54.4603 1.10582
PPP2R2B 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
RPL4 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Ranked 239.277 262.434 1.09678
360 CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured 12796.8 10886 1.17553
GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Rooted 49.3771 54.5905 1.10558
PPP2R2C 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
SEC61G protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 266.559 1.09663
361 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Measured 12787.6 10880.5 1.17528
MRPL17 mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Ranked 242.83 266.248 1.09644
RPS4Y2 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Rooted 50.7801 45.9472 1.10518
SFPQ 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 no value 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Rooted 50.7803 45.9477 1.10518
CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Measured 12786.6 10879.9 1.17525
SHROOM2 apical-like protein (apxl protein). [swissprot;acc:q13796] Ranked 231.492 211.136 1.09641
TAF7 transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Squared 57808.9 46630.3 1.23973
363 BOP1 block of proliferation 1. [swissprot;acc:q14137] Rooted 49.4884 54.6735 1.10477
CDC2 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
SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Ranked 231.481 211.131 1.09639
TAF7L 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 DDX31 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
GULP1 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Measured 5189 6088.47 1.17334
POLR2B 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
SH2D3C 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 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 17965.8 22243 1.23807
CAPS calcyphosine. [swissprot;acc:q13938] Measured 5189 6088.47 1.17334
MRPL36 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked 242.744 266.07 1.09609
NOL1 proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted 49.7541 54.9425 1.10428
366 BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared 62783.5 50784.1 1.23628
CRNKL1 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured 5189 6088.47 1.17334
RPS15A 40s ribosomal protein s15a. [swissprot;acc:p39027] Rooted 50.5463 45.7763 1.1042
RPS5 40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 242.473 265.756 1.09602
367 BHLHB5 basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared 62757.7 50767.8 1.23617
DDX18 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
HNRPM heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 234.146 256.627 1.09601
POLE 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
368 CDC40 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] 5082.66 5959.99 1.17261
DRAP1 dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared 51805.2 41916.4 1.23592
PUS1 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
RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Rooted 49.5225 54.6817 1.10418
369 CEBPZ ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Measured 3583.56 4194.95 1.17061
LGALS9 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Squared 45960.8 56749.6 1.23474
METAP1 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
MRPL12 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] Ranked 242.159 265.104 1.09475
370 EPB41 protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171] Squared 45986 56776.1 1.23464

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/