Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 2891 to 2940 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
362	CAPN1	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Rooted	Subtracted	46.8525	53.5316	6.6791
	CCNB1	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured	Divided	12786.6	10879.9	1.17525
	DVL3	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Measured	Subtracted	4981.52	5964.58	983.06
	KATNB1	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Ranked	Subtracted	232.382	252.166	19.784
	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	Ranked	Divided	231.492	211.136	1.09641
	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Squared	Divided	57808.9	46630.3	1.23973
363	no value	alpha-nac protein. [sptrembl;acc:q9h009]	Squared	Subtracted	34069.4	40333	6263.6
	BOP1	block of proliferation 1. [swissprot;acc:q14137]	Rooted	Divided	49.4884	54.6735	1.10477
	CBLB	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Measured	Subtracted	6856.71	7838.3	981.59
	CDC2	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Measured	Divided	12780.7	10876.4	1.17509
	LSM6	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Rooted	Subtracted	56.48	63.119	6.639
	SETMAR	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Ranked	Subtracted	233.539	253.197	19.658
	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Ranked	Divided	231.481	211.131	1.09639
	TAF7L	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Squared	Divided	57579.2	46497.2	1.23834
364	no value	dok-like protein. [refseq;acc:nm_024872]	Measured	Subtracted	6102.59	7081.46	978.87
	CLEC4M	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Ranked	Subtracted	233.539	253.197	19.658
	DDX31	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Rooted	Divided	50.0785	55.3215	1.1047
	DIRAS1	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Squared	Subtracted	34068.1	40330.8	6262.7
	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Rooted	Subtracted	60.594	67.2244	6.6304
	GULP1	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Measured	Divided	5189	6088.47	1.17334
	POLR2B	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Ranked		243.208	266.617	1.09625
	SH2D3C	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Squared		17957.2	22234.1	1.23817
365	BCAR3	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Squared		17965.8	22243	1.23807
	CAPS	calcyphosine. [swissprot;acc:q13938]	Measured		5189	6088.47	1.17334
	DIRAS2	di-ras2. [refseq;acc:nm_017594]	Squared	Subtracted	34068	40330.7	6262.7
	DOK2	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Measured		6102.59	7081.46	978.87
	FCER2	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Ranked		233.539	253.197	19.658
	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Ranked	Divided	242.744	266.07	1.09609
	NOL1	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Rooted	Divided	49.7541	54.9425	1.10428
	TRPC4	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Rooted	Subtracted	63.0715	56.4506	6.6209
366	ARID1A	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Squared	Subtracted	29101.9	35347	6245.1
	BHLHB4	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Squared	Divided	62783.5	50784.1	1.23628
	CD209	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Ranked	Subtracted	233.539	253.197	19.658
	CRNKL1	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Measured	Divided	5189	6088.47	1.17334
	DOK1	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Measured	Subtracted	6102.59	7081.46	978.87
	RPS15A	40s ribosomal protein s15a. [swissprot;acc:p39027]	Rooted	Divided	50.5463	45.7763	1.1042
	RPS5	40s ribosomal protein s5. [swissprot;acc:p46782]	Ranked	Divided	242.473	265.756	1.09602
	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	Rooted	Subtracted	60.6697	67.2802	6.6105
367	BHLHB5	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	Squared	Divided	62757.7	50767.8	1.23617
	DDX18	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	Rooted	Divided	49.0882	54.2027	1.10419
	DPP9	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Ranked	Subtracted	218.827	238.407	19.58
	FRK	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Measured	Subtracted	6102.59	7081.46	978.87
	HNRPM	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Ranked	Divided	234.146	256.627	1.09601
	PDCD6	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Squared	Subtracted	29101.9	35347	6245.1
	POLE	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	Measured	Divided	4024.4	4719.35	1.17268
	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Rooted	Subtracted	60.6732	67.2827	6.6095
368	ARID1B	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Squared	Subtracted	29098.8	35342.6	6243.8
	CDC40	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Measured	Divided	5082.66	5959.99	1.17261
	DPP8	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked	Subtracted	218.827	238.407	19.58
	DRAP1	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Squared	Divided	51805.2	41916.4	1.23592

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.

- http://analysis.yellowcouch.org/