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

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

Results: HTML CSV LaTeX

Showing element 2875 to 2924 of 25824 in total

Interaction Map

: High confidence
Filtered

: 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
360	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Measured	Divided	12796.8	10886	1.17553
	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Rooted		49.3771	54.5905	1.10558
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Ranked		243.072	266.559	1.09663
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Squared		9814.47	7911.48	1.24054
	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Measured	Subtracted	4590.18	5575.52	985.34
	vav-2 protein. [swissprot;acc:p52735]	Squared	Subtracted	31377.3	37670.1	6292.8
361	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Rooted	Divided	50.7801	45.9472	1.10518
	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	Rooted	Subtracted	46.8525	53.5324	6.6799
	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Measured	Subtracted	6875.08	7858.38	983.3
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Measured	Divided	12787.6	10880.5	1.17528
	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Ranked	Subtracted	232.431	252.238	19.807
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Ranked	Divided	242.83	266.248	1.09644
	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	Squared	Divided	70694.1	56989.9	1.24047
	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	Squared	Subtracted	42363.8	36083.8	6280
362	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Rooted	Divided	50.7803	45.9477	1.10518
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Ranked	Divided	231.492	211.136	1.09641
	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
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Measured	Divided	12786.6	10879.9	1.17525
	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
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Squared		34071.5	40336.5	6265
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Measured		4981.52	5964.58	983.06
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Squared	Divided	57808.9	46630.3	1.23973
363	alpha-nac protein. [sptrembl;acc:q9h009]	Squared	Subtracted	34069.4	40333	6263.6
	block of proliferation 1. [swissprot;acc:q14137]	Rooted	Divided	49.4884	54.6735	1.10477
	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
	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Ranked	Subtracted	233.539	253.197	19.658
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Ranked	Divided	231.481	211.131	1.09639
	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Measured	Subtracted	6856.71	7838.3	981.59
	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
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Rooted	Subtracted	56.48	63.119	6.639
364	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Ranked	Subtracted	233.539	253.197	19.658
	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
	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Ranked	Divided	243.208	266.617	1.09625
	dok-like protein. [refseq;acc:nm_024872]	Measured	Subtracted	6102.59	7081.46	978.87
	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Measured	Divided	5189	6088.47	1.17334
	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
	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	Divided	17957.2	22234.1	1.23817
	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Squared	Subtracted	34068.1	40330.8	6262.7
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Ranked	Divided	242.744	266.07	1.09609
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Squared		17965.8	22243	1.23807
	calcyphosine. [swissprot;acc:q13938]	Measured		5189	6088.47	1.17334
	di-ras2. [refseq;acc:nm_017594]	Squared	Subtracted	34068	40330.7	6262.7
	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Measured		6102.59	7081.46	978.87
	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
	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Rooted	Divided	49.7541	54.9425	1.10428
	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]		Subtracted	63.0715	56.4506	6.6209
366	40s ribosomal protein s15a. [swissprot;acc:p39027]		Divided	50.5463	45.7763	1.1042
	40s ribosomal protein s5. [swissprot;acc:p46782]	Ranked	Divided	242.473	265.756	1.09602
	apical-like protein (apxl protein). [swissprot;acc:q13796]	Rooted	Subtracted	60.6697	67.2802	6.6105
	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Squared	Divided	62783.5	50784.1	1.23628

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
- 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/