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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 1130 to 1179 of 12912 in total

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

Rank	Value Type	Hugo	description	red	green	network_comparison
283	Ranked	RPL11	60s ribosomal protein l11. [swissprot;acc:p39026]	241.828	267.346	1.10552
	Squared	DTX2	deltex 2. [refseq;acc:nm_020892]	6627.24	8484.19	1.2802
	Rooted	KLF5	krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887]	57.9819	64.9302	1.11984
284	Measured	PXN	paxillin. [swissprot;acc:p49023]	5221.28	6314.35	1.20935
	Ranked	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	224.657	203.235	1.10541
	Squared	CLEC3A	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	59464	76120.8	1.28012
	Rooted	CSRP1	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	51.8647	46.3161	1.1198
285	Measured	PAPOLA	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	23326.5	19296.4	1.20885
	Ranked	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	224.647	203.242	1.10532
	Squared	DTX1	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	6680.89	8549.44	1.27969
	Rooted	DDX54	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	48.4278	54.2262	1.11973
286	Measured	EXOC2	exocyst complex component sec5. [swissprot;acc:q96kp1]	23316	19288.8	1.20878
	Ranked	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]	224.633	203.251	1.1052
	Squared	PBK	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	6693.64	8564.94	1.27956
	Rooted	CSRP2	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	51.8717	46.3287	1.11965
287	Measured	PAPOLG	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	23303.1	19279.5	1.2087
	Ranked	RPS4Y2	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	240.758	266.079	1.10517
	Squared	KHDRBS3	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	6693.64	8564.94	1.27956
	Rooted	SHCBP1	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	51.8714	46.3281	1.11965
288	Measured	CPSF3	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	23422.4	19380.3	1.20857
	Ranked	no value	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	240.758	266.078	1.10517
	Squared	KHDRBS1	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559]	6693.64	8564.94	1.27956
	Rooted	CSRP3	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	51.8789	46.3416	1.11949
289	Measured	LSM6	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	4682.88	5646.19	1.20571
	Ranked	no value	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	272.781	246.892	1.10486
	Squared	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	6693.64	8564.94	1.27956
	Rooted	PRPF31	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	57.4274	64.2609	1.11899
290	Measured	TFIP11	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	4991.48	6014.08	1.20487
	Ranked	RRM2	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	231.969	210.064	1.10428
	Squared	NCBP2	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	15734.4	20126.8	1.27916
	Rooted	no value	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	75.6323	67.6572	1.11788
291	Measured	UBAC1	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	44490.5	36927.5	1.20481
	Ranked	NFYB	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]	251.679	228.037	1.10368
	Squared	CLEC3B	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	59016.1	75486.9	1.27909
	Rooted	no value	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	113.983	101.979	1.11771
292	Measured	NUBP1	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	4641.09	5588.75	1.20419
	Ranked	RPS15A	40s ribosomal protein s15a. [swissprot;acc:p39027]	241.411	266.414	1.10357
	Squared	NEURL	neuralized-like. [refseq;acc:nm_004210]	6828.26	8728.66	1.27831
	Rooted	LSM6	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	56.48	63.119	1.11755
293	Measured	NUBP2	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	4641.09	5588.75	1.20419
	Ranked	no value	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	240.782	265.717	1.10356
	Squared	KYNU	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	35991.8	46002.9	1.27815
	Rooted	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	63.0715	56.4506	1.11729
294	Measured	CSTF3	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	22515.5	18702.6	1.20387
	Ranked	BCCIP	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	240.782	265.717	1.10356
	Squared	AGPAT2	1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120]	30826.5	39383.9	1.2776
	Rooted	DVL1	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	59.0296	65.951	1.11725
295	Measured	RGL1	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	13261.9	11017.8	1.20368
	Ranked	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	223.273	202.423	1.103
	Squared	no value	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]	30807.7	39351.7	1.27733

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.