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	Network Comparison Type	Value Type	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 1325 to 1374 of 16578 in total

Value Type  : Ranked
Filtered  : 1

Rank	Hugo	description	Network Comparison Type	Interaction Map	red	network_comparison	green
332	DYNC1I1	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	Divided	Low confidence	209.495	1.03981	201.474
	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]	Subtracted	High confidence	224.633	21.382	203.251
	NEUROD6	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Divided		312	1.09859	284
	SPG20	spartin; trans-activated by hepatitis c virus core protein 1. [refseq;acc:nm_015087]	Subtracted	Low confidence	210.796	7.861	202.935
333	no value	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]		High confidence	265.634	21.33	244.304
	C20orf43	protein c20orf43 (hspc164/hspc169) (ad-007) (cda05). [swissprot;acc:q9by42]	Divided	Low confidence	200.482	1.03972	208.446
	DYNC1I2	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	Subtracted		209.221	7.841	201.38
	NEUROD1	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Divided	High confidence	312	1.09859	284
334	BICD2	coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250]		Low confidence	202.616	1.03971	194.878
	NEUROD4	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]		High confidence	312	1.09859	284
	RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Subtracted		232.473	21.266	211.207
	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]		Low confidence	199.905	7.782	192.123
335	BICD1	bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714]	Divided		202.616	1.03971	194.878
	CHD5	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]		High confidence	312	1.09859	284
	RPP30	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	Subtracted	Low confidence	202.542	7.769	210.311
	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]		High confidence	223.273	20.85	202.423
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]	Divided		312	1.09859	284
	DDOST	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]	Subtracted	Low confidence	199.343	7.753	191.59
	POLR1E	rna polymerase i associated factor 53. [refseq;acc:nm_022490]		High confidence	241.045	20.829	261.874
	TFIP11	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Divided	Low confidence	202.616	1.03971	194.878
337	no value	60s ribosomal protein l12. [swissprot;acc:p30050]		High confidence	243.583	1.0983	267.527
	CDKL1	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]		Low confidence	201.873	1.03961	194.181
	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Subtracted		212.235	7.74	204.495
	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]		High confidence	200.691	20.811	179.88
338	no value	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Divided		243.583	1.0983	267.528
	BICD2	coiled-coil protein bicd2; homolog of drosophila bicaudal d. [refseq;acc:nm_015250]	Subtracted	Low confidence	202.616	7.738	194.878
	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]		High confidence	200.691	20.811	179.88
	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Divided	Low confidence	202.572	1.03958	194.86
339	no value	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]		High confidence	243.583	1.0983	267.527
	BICD1	bicaudal d homolog 1; bicaudal-d, drosophila, homolog of, 1. [refseq;acc:nm_001714]	Subtracted	Low confidence	202.616	7.738	194.878
	DDOST	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]		High confidence	200.691	20.811	179.88
	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]	Divided	Low confidence	209.518	1.03951	201.554
340	BET1L	blocked early in transport 1 homolog (s. cerevisiae) like; golgi snare 15 kda protein. [refseq;acc:nm_016526]			201.827	1.03939	194.178
	MRPS9	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	Subtracted	High confidence	239.75	20.794	260.544
	MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	Divided		235.383	1.09811	258.476
	TFIP11	tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9]	Subtracted	Low confidence	202.616	7.738	194.878
341	no value	60s ribosomal protein l9. [swissprot;acc:p32969]	Divided	High confidence	240.243	1.09805	263.798
	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	1.03919	222.415
	UBE1C	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	Subtracted		192.088	7.714	184.374
	UQCRFSL1	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]		High confidence	240.788	20.628	261.416
342	no value	tho complex 3. [refseq;acc:nm_032361]	Divided	Low confidence	186.383	1.03907	179.374
	GALE	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376]	Subtracted		200.249	7.714	192.535
	POLR1C	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]		High confidence	240.913	20.537	261.45
	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	Divided		243.5	1.09737	267.21
343	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Subtracted		231.73	20.478	211.252
	KCNIP4	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Divided	Low confidence	213.982	1.03899	222.326
	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]		High confidence	241.625	1.0973	265.136
	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Subtracted	Low confidence	202.572	7.712	194.86
344	no value	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Divided	High confidence	241.625	1.0973	265.136
	CDKL1	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]	Subtracted	Low confidence	201.873	7.692	194.181

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.