MK5 Microarray Data

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	Value Type	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 1458 to 1507 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	description	red	green	network_comparison
365	Ranked	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	242.744	266.07	1.09609
	Squared	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	17965.8	22243	1.23807
	Rooted	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	49.7541	54.9425	1.10428
366	Measured	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	5189	6088.47	1.17334
	Ranked	40s ribosomal protein s5. [swissprot;acc:p46782]	242.473	265.756	1.09602
	Squared	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	62783.5	50784.1	1.23628
	Rooted	40s ribosomal protein s15a. [swissprot;acc:p39027]	50.5463	45.7763	1.1042
367	Measured	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	4024.4	4719.35	1.17268
	Ranked	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	234.146	256.627	1.09601
	Squared	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	62757.7	50767.8	1.23617
	Rooted	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	49.0882	54.2027	1.10419
368	Measured	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	5082.66	5959.99	1.17261
	Ranked	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	242.66	265.715	1.09501
	Squared	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	51805.2	41916.4	1.23592
	Rooted	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	49.5225	54.6817	1.10418
369	Measured	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	3583.56	4194.95	1.17061
	Ranked	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	242.159	265.104	1.09475
	Squared	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	45960.8	56749.6	1.23474
	Rooted	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	49.7435	45.0586	1.10397
370	Measured	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	4108.15	4808.93	1.17058
	Ranked	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	242.159	265.104	1.09475
	Squared	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171]	45986	56776.1	1.23464
	Rooted	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]	49.7435	45.0586	1.10397
371	Measured	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	5067.02	5926.46	1.16961
	Ranked	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	186.52	170.42	1.09447
	Squared	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]	45985.9	56776	1.23464
	Rooted	zinc finger-like protein 9. [refseq;acc:nm_033414]	49.3451	54.4606	1.10367
372	Measured	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	5067	5926.17	1.16956
	Ranked	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	186.52	170.42	1.09447
	Squared	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2]	45986.7	56776.8	1.23464
	Rooted	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]	49.3451	54.4606	1.10367
373	Measured	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	5066.99	5926.1	1.16955
	Ranked	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	242.37	265.255	1.09442
	Squared	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491]	45986	56776.1	1.23464
	Rooted	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]	49.3451	54.4606	1.10367
374	Measured	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	5066.93	5925.38	1.16942
	Ranked	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	267.208	244.168	1.09436
	Squared	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	45987	56777.1	1.23463
	Rooted	60s ribosomal protein l26. [swissprot;acc:q02877]	50.2549	45.5599	1.10305
375	Measured	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	4700.42	5492.63	1.16854
	Ranked	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	242.686	265.516	1.09407
	Squared	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5]	45987	56777.1	1.23463
	Rooted	60s ribosomal protein l35. [swissprot;acc:p42766]	50.2545	45.5637	1.10295
376	Measured	44050 protein. [refseq;acc:nm_178832]	17385.9	14889.2	1.16769
	Ranked	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	257.017	234.945	1.09395
	Squared	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	46021.4	56813.2	1.2345
	Rooted	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	50.2554	45.5688	1.10285
377	Measured	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	17385.9	14889.2	1.16769
	Ranked	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	242.691	265.481	1.09391
	Squared	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	33044.9	40781.4	1.23412

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.