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

Results: HTML CSV LaTeX

Showing element 1080 to 1129 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	green	network_comparison
270	RPS3	40s ribosomal protein s3. [swissprot;acc:p23396]	Subtracted	High confidence	241.612	265.119	23.507
271	no value	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]	Divided		241.373	267.352	1.10763
	SEC61G	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Subtracted		243.072	266.559	23.487
	TPM1	tropomyosin 1 alpha chain (alpha-tropomyosin). [swissprot;acc:p09493]		Low confidence	201.304	192.427	8.877
	TPM4	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]	Divided		201.219	192.595	1.04478
272	LGTN	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]		High confidence	241.373	267.352	1.10763
	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Subtracted		242.83	266.248	23.418
	OSR1	odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260]	Divided	Low confidence	217.69	208.421	1.04447
	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Subtracted		199.376	190.521	8.855
273	BEST1	bestrophin (vitelliform macular dystrophy protein) (tu15b). [swissprot;acc:o76090]			37.318	28.4944	8.8236
	CDC73	parafibromin. [refseq;acc:nm_024529]	Divided		214.015	204.916	1.0444
	PAPSS1	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]		High confidence	241.373	267.352	1.10763
	POLR2B	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Subtracted		243.208	266.617	23.409
274	BEST4	vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274]		Low confidence	37.3475	28.5242	8.8233
	KHDRBS3	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Divided		209.532	200.653	1.04425
	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Subtracted	High confidence	242.744	266.07	23.326
	POR	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]	Divided		241.373	267.352	1.10763
275	NCBP2L	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Low confidence	199.66	191.203	1.04423
	PCYT1B	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]		High confidence	241.373	267.352	1.10763
	RPS5	40s ribosomal protein s5. [swissprot;acc:p46782]	Subtracted		242.473	265.756	23.283
	TAF4	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]		Low confidence	202.354	211.175	8.821
276	DDX24	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]		High confidence	258.437	235.183	23.254
	NCBP2	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Divided	Low confidence	199.939	191.474	1.04421
	SNORA7A	60s ribosomal protein l32. [swissprot;acc:p02433]		High confidence	241.13	266.969	1.10716
	TAF4B	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750]	Subtracted	Low confidence	202.356	211.174	8.818
277	no value	40s ribosomal protein s29. [swissprot;acc:p30054]	Divided	High confidence	241.849	267.642	1.10665
		cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286]		Low confidence	211.912	202.965	1.04408
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted		37.9984	29.1831	8.8153
	RPL4	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]		High confidence	239.277	262.434	23.157
278	BEST2	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		Low confidence	37.9984	29.1831	8.8153
	MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]		High confidence	235.383	258.476	23.093
	RPS11	40s ribosomal protein s11. [swissprot;acc:p04643]	Divided		241.399	267.088	1.10642
	SLC7A10	asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82]		Low confidence	205.006	196.369	1.04398
279	BTBD14B	transcriptional repressor nac1. [refseq;acc:nm_052876]			202.309	211.2	1.04395
	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Subtracted		210.132	201.397	8.735
	PUS1	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]		High confidence	242.66	265.715	23.055
	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Divided		252.644	228.42	1.10605
280	LAPTM4B	lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407]	Subtracted	Low confidence	210	201.325	8.675
	MTA1	metastasis-associated protein mta1. [swissprot;acc:q13330]	Divided	High confidence	252.512	228.356	1.10578
	TFCP2L1	lbp-9. [refseq;acc:nm_014553]		Low confidence	219.758	210.509	1.04394
	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Subtracted	High confidence	267.208	244.168	23.04
281	no value	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Divided		241.808	267.335	1.10557
	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	Subtracted		242.159	265.104	22.945
	TFCP2	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Divided	Low confidence	219.749	210.503	1.04392
	TMEM115	pl6 protein (placental protein 6). [swissprot;acc:q12893]	Subtracted		209.995	201.322	8.673
282	AMY1C	alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]	Divided		219.742	210.498	1.04391
	LAPTM4A	lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012]	Subtracted		209.995	201.322	8.673
	NUDT12	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]		High confidence	242.159	265.104	22.945
	RBBP4	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]	Divided		252.39	228.297	1.10553
283	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Subtracted	Low confidence	209.31	200.66	8.65

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.