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	Value Type	description	Hugo	Interaction Map	network_comparison	Filtered	red	green

Results: HTML CSV LaTeX

Showing element 59524 to 59573 of 66312 in total

Network Comparison Type  : Subtracted
Interaction Map  : Low confidence
Filtered  : 1

Rank	Value Type	description	Hugo	network_comparison	red	green
3364	Rooted	poly(rc)-binding protein 1 (alpha-cp1) (hnrnp-e1) (nucleic acid binding protein sub2.3). [swissprot;acc:q15365]	PCBP1	2.2117	71.0076	73.2193
3365	Measured	gamma-tubulin complex component 3 (gcp-3) (spindle pole body protein spc98 homolog) (hspc98) (hgcp3) (h104p). [swissprot;acc:q96cw5]	TUBGCP3	211.76	8036.77	8248.53
	Ranked	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	STAM	3.057	201.985	198.928
	Squared	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	GPT	1444.8	50292.4	51737.2
	Rooted	lim domain only 7; zinc-finger domain-containing protein; lomp protein; f-box only protein 20; f-box protein fbx20. [refseq;acc:nm_005358]	LMO7	2.2111	71.2279	73.439
3366	Measured	nadh-ubiquinone oxidoreductase subunit b14.5a (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14.5a) (ci-b14.5a). [swissprot;acc:o95182]	NDUFA7	211.71	7723.4	7935.11
	Ranked	calcium-binding mitochondrial carrier protein aralar1 (solute carrier family 25, member 12). [swissprot;acc:o75746]	SLC25A12	3.053	197.815	194.762
	Squared	ubiquinol-cytochrome c reductase complex core protein 2, mitochondrial precursor (ec 1.10.2.2) (complex iii subunit ii). [swissprot;acc:p22695]	UQCRC2	1444.7	43630.9	42186.2
	Rooted	cytosolic ovarian carcinoma antigen 1 (apk1 antigen). [swissprot;acc:q16206]	ENOX2	2.2102	71.5541	73.7643
3367	Measured	aconitate hydratase, mitochondrial precursor (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:q99798]	ACO2	211.68	8312.07	8523.75
	Ranked	hmg-box transcription factor bbx; x 001 protein. [refseq;acc:nm_020235]	BBX	3.052	201.412	198.36
	Squared	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318]	MAP3K7	1444.7	43630.9	42186.2
	Rooted	nanos (fragment). [sptrembl;acc:q8wy41]	no value	2.2086	68.6835	66.4749
3368	Measured	forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488]	FOXG1	211.67	7848.98	8060.65
	Ranked	erythroid differentiation-related factor 1. [refseq;acc:nm_015608]	C10orf137	3.051	200.658	197.607
	Squared	vacuolar atp synthase subunit c (ec 3.6.3.14) (v-atpase c subunit) (vacuolar proton pump c subunit). [swissprot;acc:p21283]	ATP6V1C1	1444.6	45316.6	43872
	Rooted	cell division cycle 2-like protein kinase 5 (ec 2.7.1.-) (cholinesterase-related cell division controller) (cdc2-related protein kinase 5). [swissprot;acc:q14004]	CDC2L5	2.2083	71.2557	73.464
3369	Measured	acetyl-coenzyme a transporter. [refseq;acc:nm_004733]	SLC33A1	211.61	8144.55	8356.16
	Ranked	amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380]	APPBP2	3.051	200.658	197.607
	Squared	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	CDK2AP2	1443.9	40023.6	38579.7
	Rooted	ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794]	FTH1	2.208	70.9882	73.1962
3370	Measured	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	ZNRD1	211.61	8144.55	8356.16
	Ranked	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347]	EIF3I	3.049	199.38	196.331
	Squared	rtp801. [refseq;acc:nm_019058]	DDIT4	1443.6	48707.8	47264.2
	Rooted	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	POLR1B	2.2075	72.0185	74.226
3371	Measured	vps10 domain-containing receptor sorcs2 precursor. [swissprot;acc:q96pq0]	SORCS2	211.55	8640.27	8851.82
	Ranked	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	CPE	3.048	201.399	198.351
	Squared	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	CHD3	1443.5	40879.6	39436.1
	Rooted	transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354]	TADA3L	2.2065	72.4843	74.6908
3372	Measured	vps10 domain-containing receptor sorcs3 precursor. [swissprot;acc:q9upu3]	SORCS3	211.55	8640.27	8851.82
	Ranked	cappuccino. [refseq;acc:nm_018366]	CNO	3.047	202.766	199.719
	Squared	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	CHD5	1443.5	40878.5	39435
	Rooted	mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478]	FTMT	2.206	70.9897	73.1957
3373	Measured	sortilin-related receptor precursor (sorting protein-related receptor containing ldlr class a repeats) (sorla) (sorla-1) (low-density lipoprotein receptor relative with 11 ligand-binding repeats) (ldlr relative with 11 ligand-binding repeats) (lr11). [swissprot;acc:q92673]	SORL1	211.55	8640.27	8851.82
	Ranked	nucleoporin 54kda; nucleoporin p54. [refseq;acc:nm_017426]	NUP54	3.047	202.766	199.719
	Squared	mitochondrial ribosomal protein l44. [refseq;acc:nm_022915]	MRPL44	1442.6	41143.4	39700.8
	Rooted	ring finger protein 111; arkadia. [refseq;acc:nm_017610]	RNF111	2.2057	71.0372	73.2429
3374	Measured	vps10 domain-containing receptor sorcs1 precursor (hsorcs). [swissprot;acc:q8wy21]	SORCS1	211.55	8640.27	8851.82
	Ranked	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	LSM8	3.047	204.036	200.989
	Squared	similar to smhs1 protein. [refseq;acc:nm_145244]	DDIT4L	1440.6	48866.7	47426.1
	Rooted	rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9]	RBM38	2.2057	71.0364	73.2421
3375	Measured	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	MVD	211.41	7955.52	8166.93
	Ranked	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [swissprot;acc:q9ulu4]	ZMYND8	3.047	202.081	199.034
	Squared	ankyrin repeat and btb (poz) domain containing 1 isoform 1; elongation factor 1a binding protein. [refseq;acc:nm_032548]	ABTB1	1440.5	44401.5	42961
	Rooted	ubiquitin and ribosomal protein s27a precursor; ubiquitin carboxyl extension protein 80; 40s ribosomal protein s27a; ubiquitin; ubiquitin-cep80. [refseq;acc:nm_002954]	no value	2.2053	71.9777	74.183
3376	Measured	calcium/calmodulin-dependent protein kinase kinase 2 beta isoform 1; camkk beta protein; calcium/calmodulin-dependent protein kinase beta. [refseq;acc:nm_006549]	CAMKK2	211.41	8137.16	8348.57
	Ranked	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	PCF11	3.044	194.562	191.518
	Squared	ring-box 1; ring box protein 1; regulator of cullins 1; ring finger protein; zyp protein. [refseq;acc:nm_014248]	RBX1	1440.5	44401.5	42961
	Rooted	ptd012 protein. [refseq;acc:nm_014039]	C11orf54	2.2052	71.978	74.1832
3377	Measured	dnaj (hsp40) homolog, subfamily c, member 3; protein-kinase, interferon-inducible double stranded rna dependent inhibitor. [refseq;acc:nm_006260]	DNAJC3	211.41	7955.52	8166.93

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.