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

Results: HTML CSV LaTeX

Showing element 1332 to 1381 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	description	Hugo	Network Comparison Type	Interaction Map	red	network_comparison	green
333	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	no value	Subtracted	High confidence	265.634	21.33	244.304
334	coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250]	BICD2	Divided	Low confidence	202.616	1.03971	194.878
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	NEUROD4		High confidence	312	1.09859	284
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	RRM2B	Subtracted		232.473	21.266	211.207
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	STT3B		Low confidence	199.905	7.782	192.123
335	bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714]	BICD1	Divided		202.616	1.03971	194.878
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	CHD5		High confidence	312	1.09859	284
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	SCYE1	Subtracted		223.273	20.85	202.423
	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	RPP30		Low confidence	202.542	7.769	210.311
336	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]	CDK2AP1	Divided	High confidence	312	1.09859	284
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	DDOST	Subtracted	Low confidence	199.343	7.753	191.59
	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	POLR1E		High confidence	241.045	20.829	261.874
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	TFIP11	Divided	Low confidence	202.616	1.03971	194.878
337	60s ribosomal protein l12. [swissprot;acc:p30050]	no value		High confidence	243.583	1.0983	267.527
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	DGCR14	Subtracted	Low confidence	212.235	7.74	204.495
	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]	CDKL1	Divided		201.873	1.03961	194.181
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	STT3B	Subtracted	High confidence	200.691	20.811	179.88
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	no value	Divided		243.583	1.0983	267.528
	coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250]	BICD2	Subtracted	Low confidence	202.616	7.738	194.878
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	STT3A		High confidence	200.691	20.811	179.88
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	TXNL4A	Divided	Low confidence	202.572	1.03958	194.86
339	bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714]	BICD1	Subtracted		202.616	7.738	194.878
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	no value	Divided	High confidence	243.583	1.0983	267.527
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	DDOST	Subtracted		200.691	20.811	179.88
	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]	GGPS1	Divided	Low confidence	209.518	1.03951	201.554
340	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	MRPS9	Subtracted	High confidence	239.75	20.794	260.544
	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]	BET1L	Divided	Low confidence	201.827	1.03939	194.178
	myelin gene expression factor 2. [refseq;acc:nm_016132]	MYEF2		High confidence	235.383	1.09811	258.476
	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	TFIP11	Subtracted	Low confidence	202.616	7.738	194.878
341	60s ribosomal protein l9. [swissprot;acc:p32969]	no value	Divided	High confidence	240.243	1.09805	263.798
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	KCNIP1		Low confidence	214.027	1.03919	222.415
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	UQCRFSL1	Subtracted	High confidence	240.788	20.628	261.416
	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	UBE1C		Low confidence	192.088	7.714	184.374
342	40s ribosomal protein s20. [swissprot;acc:p17075]	RPS20	Divided	High confidence	243.5	1.09737	267.21
	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	POLR1C	Subtracted		240.913	20.537	261.45
	tho complex 3. [refseq;acc:nm_032361]	no value	Divided	Low confidence	186.383	1.03907	179.374
	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]	GALE	Subtracted		200.249	7.714	192.535
343	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	KCNIP4	Divided		213.982	1.03899	222.326
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	PRMT3		High confidence	241.625	1.0973	265.136
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	GIPC1	Subtracted		231.73	20.478	211.252
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	TXNL4A		Low confidence	202.572	7.712	194.86
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	no value	Divided	High confidence	241.625	1.0973	265.136
	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	POLR1B	Subtracted		240.6	20.441	261.041
	mitochondrial ribosomal protein l44. [refseq;acc:nm_022915]	MRPL44	Divided	Low confidence	216.283	1.03896	208.173
	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]	CDKL1	Subtracted		201.873	7.692	194.181
345	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]	KCNIP2	Divided		213.976	1.03896	222.312
	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	EGFL8	Subtracted		214.628	7.673	222.301
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	no value		High confidence	224.445	20.401	204.044
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	CMPK	Divided		242.14	1.09729	265.697
346	40s ribosomal protein s3. [swissprot;acc:p23396]	RPS3			241.612		265.119

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.