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

Results: HTML CSV LaTeX

Showing element 2880 to 2929 of 25824 in total

Filtered

: 1
Interaction Map

: High confidence

Rank	Value Type	description	Network Comparison Type	red	green	network_comparison
360	Rooted	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Divided	49.3771	54.5905	1.10558
361	Measured	cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681]	Subtracted	6875.08	7858.38	983.3
	Measured	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Divided	12787.6	10880.5	1.17528
	Ranked	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Subtracted	232.431	252.238	19.807
	Ranked	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Divided	242.83	266.248	1.09644
	Squared	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]	Divided	70694.1	56989.9	1.24047
	Squared	translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693]	Subtracted	42363.8	36083.8	6280
	Rooted	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Divided	50.7801	45.9472	1.10518
	Rooted	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]	Subtracted	46.8525	53.5324	6.6799
362	Measured	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Divided	12786.6	10879.9	1.17525
	Measured	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Subtracted	4981.52	5964.58	983.06
	Ranked	apical-like protein (apxl protein). [swissprot;acc:q13796]	Divided	231.492	211.136	1.09641
	Ranked	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Subtracted	232.382	252.166	19.784
	Squared	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Subtracted	34071.5	40336.5	6265
	Squared	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Divided	57808.9	46630.3	1.23973
	Rooted	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	Divided	50.7803	45.9477	1.10518
	Rooted	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Subtracted	46.8525	53.5316	6.6791
363	Measured	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Divided	12780.7	10876.4	1.17509
	Measured	signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191]	Subtracted	6856.71	7838.3	981.59
	Ranked	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	Subtracted	233.539	253.197	19.658
	Ranked	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Divided	231.481	211.131	1.09639
	Squared	alpha-nac protein. [sptrembl;acc:q9h009]	Subtracted	34069.4	40333	6263.6
	Squared	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]	Divided	57579.2	46497.2	1.23834
	Rooted	block of proliferation 1. [swissprot;acc:q14137]	Divided	49.4884	54.6735	1.10477
	Rooted	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Subtracted	56.48	63.119	6.639
364	Measured	dok-like protein. [refseq;acc:nm_024872]	Subtracted	6102.59	7081.46	978.87
	Measured	ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315]	Divided	5189	6088.47	1.17334
	Ranked	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	Subtracted	233.539	253.197	19.658
	Ranked	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Divided	243.208	266.617	1.09625
	Squared	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]	Divided	17957.2	22234.1	1.23817
	Squared	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Subtracted	34068.1	40330.8	6262.7
	Rooted	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	Divided	50.0785	55.3215	1.1047
	Rooted	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	Subtracted	60.594	67.2244	6.6304
365	Measured	calcyphosine. [swissprot;acc:q13938]	Divided	5189	6088.47	1.17334
	Measured	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Subtracted	6102.59	7081.46	978.87
	Ranked	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Divided	242.744	266.07	1.09609
	Ranked	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Subtracted	233.539	253.197	19.658
	Squared	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Divided	17965.8	22243	1.23807
	Squared	di-ras2. [refseq;acc:nm_017594]	Subtracted	34068	40330.7	6262.7
	Rooted	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Divided	49.7541	54.9425	1.10428
	Rooted	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	Measured	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Divided	5189	6088.47	1.17334
	Measured	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Subtracted	6102.59	7081.46	978.87
	Ranked	40s ribosomal protein s5. [swissprot;acc:p46782]	Divided	242.473	265.756	1.09602
	Ranked	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	Subtracted	233.539	253.197	19.658
	Squared	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	Divided	62783.5	50784.1	1.23628
	Squared	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Subtracted	29101.9	35347	6245.1
	Rooted	40s ribosomal protein s15a. [swissprot;acc:p39027]	Divided	50.5463	45.7763	1.1042
	Rooted	apical-like protein (apxl protein). [swissprot;acc:q13796]	Subtracted	60.6697	67.2802	6.6105
367	Measured	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	Divided	4024.4	4719.35	1.17268

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/