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 658 to 707 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
329	NEUROD2	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Divided	312	284	1.09859
330	BCAR1	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	Subtracted	224.657	203.235	21.422
	CHD3	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	Divided	312	284	1.09859
331	CCT4	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Subtracted	224.647	203.242	21.405
	CDK2AP2	doc-1 related protein (doc-1r). [swissprot;acc:o75956]	Divided	312	284	1.09859
332	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	224.633	203.251	21.382
	NEUROD6	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Divided	312	284	1.09859
333	no value	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Subtracted	265.634	244.304	21.33
	NEUROD1	neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]	Divided	312	284	1.09859
334	NEUROD4	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]
	RRM2B	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Subtracted	232.473	211.207	21.266
335	CHD5	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Divided	312	284	1.09859
	SCYE1	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Subtracted	223.273	202.423	20.85
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	284	1.09859
	POLR1E	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Subtracted	241.045	261.874	20.829
337	no value	60s ribosomal protein l12. [swissprot;acc:p30050]	Divided	243.583	267.527	1.0983
	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Subtracted	200.691	179.88	20.811
338	no value	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Divided	243.583	267.528	1.0983
	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Subtracted	200.691	179.88	20.811
339	no value	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Divided	243.583	267.527	1.0983
	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	200.691	179.88	20.811
340	MRPS9	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]		239.75	260.544	20.794
	MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	Divided	235.383	258.476	1.09811
341	no value	60s ribosomal protein l9. [swissprot;acc:p32969]		240.243	263.798	1.09805
	UQCRFSL1	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Subtracted	240.788	261.416	20.628
342	POLR1C	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]		240.913	261.45	20.537
	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	Divided	243.5	267.21	1.09737
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	211.252	20.478
	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Divided	241.625	265.136	1.0973
344	no value	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
	POLR1B	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	Subtracted	240.6	261.041	20.441
345	no value	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]		224.445	204.044	20.401
	CMPK	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Divided	242.14	265.697	1.09729
346	RPS3	40s ribosomal protein s3. [swissprot;acc:p23396]		241.612	265.119
	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	Subtracted	231.492	211.136	20.356
347	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	Divided	242.14	265.697	1.09729
	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Subtracted	231.481	211.131	20.35
348	no value	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	Divided	242.14	265.696	1.09728
	SLC15A2	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Subtracted	185.969	165.623	20.346
349	CEBPZ	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]		255.112	234.804	20.308
	MED22	surfeit locus protein 5. [swissprot;acc:q15528]	Divided	242.14	265.696	1.09728
350	no value	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Subtracted	233.376	253.539	20.163
	SCAPER	zinc finger protein 291. [swissprot;acc:q9by12]	Divided	242.14	265.696	1.09728
351	GTF2H1	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Subtracted	233.376	253.539	20.163
	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	Divided	242.14	265.696	1.09728
352	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	Subtracted	237.862	217.739	20.123
	TXNDC9	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	Divided	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
	STAMBPL1	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Subtracted	94	114	20
354	CHMP2A	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]

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.