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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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Network Comparison Type	Rank	Gene	Hugo	description	Value Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 180 to 229 of 6640 in total

Network Comparison Type  : Divided
Hugo  : no value
Filtered  : 1

Rank	description	Value Type	Interaction Map	red	green	network_comparison
250	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Measured	High confidence	6417.18	7859.6	1.22477
256	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Squared		15465.1	20151	1.303
257	cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286]	Rooted	Low confidence	68.3669	72.2396	1.05665
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared	High confidence	15482.3	20162.4	1.30229
263	sodium/hydrogen exchanger 6 (na(+)/h(+) exchanger 6) (nhe-6). [swissprot;acc:q92581]	Ranked	Low confidence	216.546	207.063	1.0458
268	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Rooted	High confidence	66.1064	74.1074	1.12103
271	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Ranked		241.373	267.352	1.10763
275	adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]	Rooted	Low confidence	70.162	74.0605	1.05556
277	40s ribosomal protein s29. [swissprot;acc:p30054]	Ranked	High confidence	241.849	267.642	1.10665
	casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	Squared	Low confidence	51230.9	47140.4	1.08677
	cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286]	Ranked		211.912	202.965	1.04408
278	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Measured		7762.96	8229.42	1.06009
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Squared	High confidence	16120.1	20665.7	1.28198
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Rooted		65.9938	73.9449	1.12048
280	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]			57.9068	64.8562	1.12001
281	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Ranked		241.808	267.335	1.10557
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]			240.758	266.078	1.10517
289	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]			272.781	246.892	1.10486
290	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Rooted		75.6323	67.6572	1.11788
291	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]			113.983	101.979	1.11771
293	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Ranked		240.782	265.717	1.10356
295	1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943]	Squared		30807.7	39351.7	1.27733
297	60s ribosomal protein l7. [swissprot;acc:p18124]	Ranked		235.727	259.984	1.1029
298	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Squared		14247.4	18142.1	1.27336
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Measured		4633.92	5572.85	1.20262
299	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]			4914.27	5907.12	1.20203
300	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Rooted	Low confidence	70.2592	74.0161	1.05347
301	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Measured	High confidence	13768.2	11466	1.20078
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	Rooted		203.673	182.638	1.11517
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Squared		28896.2	36767	1.27238
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Ranked		242.339	266.986	1.1017
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]			242.153	266.673	1.10126
	pnas-18. [sptrembl;acc:q9bzu3]	Measured		13680.5	11409.6	1.19903
309	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Ranked	Low confidence	200.213	192.103	1.04222
	u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Rooted	High confidence	56.185	62.6036	1.11424
310	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]			95.0526	85.3206	1.11406
312	methyltransferase like 2. [refseq;acc:nm_018396]	Squared		71576.8	56326.7	1.27074
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Measured		4598.21	5500.48	1.19622
313	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Ranked	Low confidence	202.05	193.94	1.04182
	endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759]	Squared		51313.9	47442	1.08161
316	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Rooted	High confidence	95.0526	85.3206	1.11406
317	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Ranked		224.445	204.044	1.09998
318	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Measured		34190.9	40795.8	1.19318
320	40s ribosomal protein s29. [swissprot;acc:p30054]	Rooted		50.2784	45.294	1.11005
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Ranked		241.892	265.959	1.09949
	u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45]	Rooted		55.9231	62.0565	1.10968
322	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]		Low confidence	69.9808	73.647	1.05239
323	60s ribosomal protein l23a. [swissprot;acc:p29316]	Ranked	High confidence	241.884	265.945	1.09947
	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	Squared		33514.4	42370.8	1.26426
325	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Rooted		50.3803	45.4193	1.10923

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.