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	Hugo	Value Type	description	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 1108 to 1157 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	Network Comparison Type	Hugo	description	Interaction Map	red	network_comparison	green
277	Subtracted	RPL4	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	High confidence	239.277	23.157	262.434
278	Divided	RPS11	40s ribosomal protein s11. [swissprot;acc:p04643]		241.399	1.10642	267.088
		SLC7A10	asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82]	Low confidence	205.006	1.04398	196.369
	Subtracted	BEST2	vitelliform macular dystrophy 2-like protein 1. [refseq;acc:nm_017682]		37.9984	8.8153	29.1831
		MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	High confidence	235.383	23.093	258.476
279	Divided	BTBD14B	transcriptional repressor nac1. [refseq;acc:nm_052876]	Low confidence	202.309	1.04395	211.2
		RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	High confidence	252.644	1.10605	228.42
	Subtracted	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Low confidence	210.132	8.735	201.397
		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	23.055	265.715
280	Divided	MTA1	metastasis-associated protein mta1. [swissprot;acc:q13330]		252.512	1.10578	228.356
		TFCP2L1	lbp-9. [refseq;acc:nm_014553]	Low confidence	219.758	1.04394	210.509
	Subtracted	LAPTM4B	lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407]		210	8.675	201.325
		TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	High confidence	267.208	23.04	244.168
281	Divided	no value	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]		241.808	1.10557	267.335
		TFCP2	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Low confidence	219.749	1.04392	210.503
	Subtracted	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	High confidence	242.159	22.945	265.104
		TMEM115	pl6 protein (placental protein 6). [swissprot;acc:q12893]	Low confidence	209.995	8.673	201.322
282	Divided	AMY1C	alpha-amylase, salivary precursor (ec 3.2.1.1) (1,4-alpha-d-glucan glucanohydrolase). [swissprot;acc:p04745]		219.742	1.04391	210.498
		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]	High confidence	252.39	1.10553	228.297
	Subtracted	LAPTM4A	lysosomal-associated transmembrane protein 4a (golgi 4-transmembrane spanning transporter mtp). [swissprot;acc:q15012]	Low confidence	209.995	8.673	201.322
		NUDT12	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	High confidence	242.159	22.945	265.104
283	Divided	RPL11	60s ribosomal protein l11. [swissprot;acc:p39026]		241.828	1.10552	267.346
		UBP1	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	Low confidence	219.722	1.04389	210.484
	Subtracted	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]		209.31	8.65	200.66
		MRPL11	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	High confidence	242.37	22.885	265.255
284	Divided	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]		224.657	1.10541	203.235
		TNKS2	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]	Low confidence	214.675	1.04367	205.692
	Subtracted	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	High confidence	242.686	22.83	265.516
		SLC7A10	asc-type amino acid transporter 1 (asc-1). [swissprot;acc:q9ns82]	Low confidence	205.006	8.637	196.369
285	Divided	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	High confidence	224.647	1.10532	203.242
		TAF4	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Low confidence	202.354	1.04359	211.175
	Subtracted	POLR1A	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	High confidence	242.691	22.79	265.481
		TPM4	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]	Low confidence	201.219	8.624	192.595
286	Divided	NEDD9	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]	High confidence	224.633	1.1052	203.251
		TAF4B	transcription initiation factor tfiid 105 kda subunit (tafii-105) (tafii105) (fragment). [swissprot;acc:q92750]	Low confidence	202.356	1.04358	211.174
	Subtracted	HOMER3	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]		210.057	8.607	201.45
		RPL30	60s ribosomal protein l30. [swissprot;acc:p04645]	High confidence	242.593	22.772	265.365
287	Divided	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Low confidence	210.132	1.04337	201.397
		RPS4Y2	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	High confidence	240.758	1.10517	266.079
	Subtracted	HOMER1	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Low confidence	210.05	8.596	201.454
		SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	High confidence	225.217	22.758	202.459
288	Divided	no value	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]		240.758	1.10517	266.078
		SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Low confidence	200.288	1.04314	192.004
	Subtracted	DICER1	endoribonuclease dicer (ec 3.1.26.-) (helicase with rnase motif) (helicase-moi). [swissprot;acc:q9upy3]		208.915	8.593	200.322
		STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	High confidence	234.691	22.751	257.442
289	Divided	no value	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]		272.781	1.10486	246.892
		KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Low confidence	209.31	1.04311	200.66
	Subtracted	DNASE2B	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]		57.395	8.5764	48.8186
		STX6	syntaxin 6. [swissprot;acc:o43752]	High confidence	234.673	22.741	257.414
290	Divided	LAPTM4B	lysosomal-associated transmembrane protein 4 beta; putative integral membrane transporter. [refseq;acc:nm_018407]	Low confidence	210	1.04309	201.325

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.