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 663 to 712 of 8289 in total

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

Rank	Hugo	description	Interaction Map	red	green	network_comparison
332	DYNC1I1	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	Low confidence	209.495	201.474	1.03981
	NEUROD6	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	High confidence	312	284	1.09859
333	C20orf43	protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42]	Low confidence	200.482	208.446	1.03972
	NEUROD1	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	High confidence	312	284	1.09859
334	BICD2	coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250]	Low confidence	202.616	194.878	1.03971
	NEUROD4	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	High confidence	312	284	1.09859
335	BICD1	bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714]	Low confidence	202.616	194.878	1.03971
	CHD5	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	High confidence	312	284	1.09859
336	CDK2AP1	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]
	TFIP11	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Low confidence	202.616	194.878	1.03971
337	no value	60s ribosomal protein l12. [swissprot;acc:p30050]	High confidence	243.583	267.527	1.0983
	CDKL1	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]	Low confidence	201.873	194.181	1.03961
338	no value	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	High confidence	243.583	267.528	1.0983
	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Low confidence	202.572	194.86	1.03958
339	no value	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	High confidence	243.583	267.527	1.0983
	GGPS1	geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749]	Low confidence	209.518	201.554	1.03951
340	BET1L	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]		201.827	194.178	1.03939
	MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	High confidence	235.383	258.476	1.09811
341	no value	60s ribosomal protein l9. [swissprot;acc:p32969]		240.243	263.798	1.09805
	KCNIP1	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Low confidence	214.027	222.415	1.03919
342	no value	tho complex 3. [refseq;acc:nm_032361]		186.383	179.374	1.03907
	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	High confidence	243.5	267.21	1.09737
343	KCNIP4	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Low confidence	213.982	222.326	1.03899
	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	High confidence	241.625	265.136	1.0973
344	no value	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
	MRPL44	mitochondrial ribosomal protein l44. [refseq;acc:nm_022915]	Low confidence	216.283	208.173	1.03896
345	CMPK	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	High confidence	242.14	265.697	1.09729
	KCNIP2	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Low confidence	213.976	222.312	1.03896
346	DYNC1I2	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]		209.221	201.38	1.03894
	RPS3	40s ribosomal protein s3. [swissprot;acc:p23396]	High confidence	241.612	265.119	1.09729
347	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]		242.14	265.697
	NME7	nucleoside diphosphate kinase 7 (ec 2.7.4.6) (ndk 7) (ndp kinase 7) (nm23-h7). [swissprot;acc:q9y5b8]	Low confidence	210.796	202.935	1.03874
348	no value	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	High confidence	242.14	265.696	1.09728
	SPG20	spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087]	Low confidence	210.796	202.935	1.03874
349	AP2A2	adapter-related protein complex 2 alpha 2 subunit (alpha-adaptin c) (clathrin assembly protein complex 2 alpha-c large chain) (100 kda coated vesicle protein c) (plasma membrane adaptor ha2/ap2 adaptin alpha c subunit) (huntingtin-interacting protein hypj). [swissprot;acc:o94973]		204.762	197.135	1.03869
	MED22	surfeit locus protein 5. [swissprot;acc:q15528]	High confidence	242.14	265.696	1.09728
350	PUF60	fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281]	Low confidence	204.762	197.135	1.03869
	SCAPER	zinc finger protein 291. [swissprot;acc:q9by12]	High confidence	242.14	265.696	1.09728
351	AP2S1	clathrin coat assembly protein ap17 (clathrin coat associated protein ap17) (plasma membrane adaptor ap-2 17 kda protein) (ha2 17 kda subunit) (clathrin assembly protein 2 small chain). [swissprot;acc:p53680]	Low confidence	204.762	197.135	1.03869
	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	High confidence	242.14	265.696	1.09728
352	no value	adapter-related protein complex 2 alpha 1 subunit (alpha-adaptin a) (adaptor protein complex ap-2 alpha-1 subunit) (clathrin assembly protein complex 2 alpha-a large chain) (100 kda coated vesicle protein a) (plasma membrane adaptor ha2/ap2 adaptin alpha a subunit). [swissprot;acc:o95782]	Low confidence	204.762	197.135	1.03869
	TXNDC9	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	High confidence	242.14	265.696	1.09728
353	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]		231.73	211.252	1.09694
	UBE2G1	ubiquitin-conjugating enzyme e2 g1 (ec 6.3.2.19) (ubiquitin-protein ligase g1) (ubiquitin carrier protein g1) (e217k) (ubc7). [swissprot;acc:q99462]	Low confidence	202.962	195.416	1.03862
354	COG3	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]		206.433	198.781	1.03849
	STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	High confidence	234.691	257.442	1.09694
355	RPP30	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	Low confidence	202.542	210.311	1.03836
	STX6	syntaxin 6. [swissprot;acc:o43752]	High confidence	234.673	257.414	1.09691
356	no value	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]		243.24	266.796	1.09684
	SF3A3	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Low confidence	202.387	194.949	1.03815

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.