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

Results: HTML CSV LaTeX

Showing element 532 to 581 of 8289 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1

Rank	description	Hugo	Interaction Map	red	green	network_comparison
266	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	SIN3A	High confidence	241.07	267.88	1.11121
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	DENR
	tensin. [refseq;acc:nm_022648]	TNS1	Low confidence	215.258	205.872	1.04559
268	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	EIF5	High confidence	271.016	244.167	1.10996
	sterol o-acyltransferase 2 (ec 2.3.1.26) (cholesterol acyltransferase 2) (acyl coenzyme a:cholesterol acyltransferase 2) (acat-2). [swissprot;acc:o75908]	SOAT2	Low confidence	208.469	199.455	1.04519
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	PCYT1A	High confidence	241.373	267.352	1.10763
	sterol o-acyltransferase 1 (ec 2.3.1.26) (cholesterol acyltransferase 1) (acyl coenzyme a:cholesterol acyltransferase 1) (acat-1). [swissprot;acc:p35610]	SOAT1	Low confidence	208.436	199.44	1.04511
270	fad synthetase. [refseq;acc:nm_025207]	FLAD1	High confidence	241.373	267.352	1.10763
	ring finger protein 10. [refseq;acc:nm_014868]	RNF10	Low confidence	208.437	199.44	1.04511
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]	no value	High confidence	241.373	267.352	1.10763
	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]	TPM4	Low confidence	201.219	192.595	1.04478
272	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]	LGTN	High confidence	241.373	267.352	1.10763
	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	OSR1	Low confidence	217.69	208.421	1.04447
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252]	PAPSS1	High confidence	241.373	267.352	1.10763
	parafibromin. [refseq;acc:nm_024529]	CDC73	Low confidence	214.015	204.916	1.0444
274	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	KHDRBS3		209.532	200.653	1.04425
	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	POR	High confidence	241.373	267.352	1.10763
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	PCYT1B
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	NCBP2L	Low confidence	199.66	191.203	1.04423
276	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	NCBP2		199.939	191.474	1.04421
	60s ribosomal protein l32. [swissprot;acc:p02433]	SNORA7A	High confidence	241.13	266.969	1.10716
277	40s ribosomal protein s29. [swissprot;acc:p30054]	no value		241.849	267.642	1.10665
	cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286]		Low confidence	211.912	202.965	1.04408
278	40s ribosomal protein s11. [swissprot;acc:p04643]	RPS11	High confidence	241.399	267.088	1.10642
	asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82]	SLC7A10	Low confidence	205.006	196.369	1.04398
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	RBBP7	High confidence	252.644	228.42	1.10605
	transcriptional repressor nac1. [refseq;acc:nm_052876]	BTBD14B	Low confidence	202.309	211.2	1.04395
280	lbp-9. [refseq;acc:nm_014553]	TFCP2L1		219.758	210.509	1.04394
	metastasis-associated protein mta1. [swissprot;acc:q13330]	MTA1	High confidence	252.512	228.356	1.10578
281	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	no value		241.808	267.335	1.10557
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	TFCP2	Low confidence	219.749	210.503	1.04392
282	alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]	AMY1C		219.742	210.498	1.04391
	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	RBBP4	High confidence	252.39	228.297	1.10553
283	60s ribosomal protein l11. [swissprot;acc:p39026]	RPL11		241.828	267.346	1.10552
	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	UBP1	Low confidence	219.722	210.484	1.04389
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	BCAR1	High confidence	224.657	203.235	1.10541
	tankyrase 2 (ec 2.4.2.30) (tank2) (tankyrase ii) (tnks-2) (trf1- interacting ankyrin-related adp-ribose polymerase 2) (tankyrase-like protein) (tankyrase-related protein). [swissprot;acc:q9h2k2]	TNKS2	Low confidence	214.675	205.692	1.04367
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	CCT4	High confidence	224.647	203.242	1.10532
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	TAF4	Low confidence	202.354	211.175	1.04359
286	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	NEDD9	High confidence	224.633	203.251	1.1052
	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750]	TAF4B	Low confidence	202.356	211.174	1.04358
287	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	RPS4Y2	High confidence	240.758	266.079	1.10517
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	GIPC1	Low confidence	210.132	201.397	1.04337
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	no value	High confidence	240.758	266.078	1.10517
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	SNRPD1	Low confidence	200.288	192.004	1.04314
289	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	no value	High confidence	272.781	246.892	1.10486
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	KHDRBS2	Low confidence	209.31	200.66	1.04311
290	lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407]	LAPTM4B		210	201.325	1.04309
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	RRM2	High confidence	231.969	210.064	1.10428
291	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	NFYB		251.679	228.037	1.10368

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.