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.

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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 980 to 1029 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
123	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Rooted	Divided	54.6527	67.9743	1.24375
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Ranked		269.23	327.601	1.21681
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Measured	Subtracted	4942.49	7037.32	2094.83
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Squared	Divided	192904	126167	1.52896
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Ranked	Subtracted	227.032	193.056	33.976
124	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	Squared		71389.9	96037.6	24647.7
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	Rooted		46.7419	60.9337	14.1918
	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Measured		4944.3	7038.04	2093.74
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	Ranked	Divided	208.52	171.595	1.21519
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Measured		24255.7	18168.9	1.33501
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Rooted		54.6625	67.9477	1.24304
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Ranked	Subtracted	285.684	252.234	33.45
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	Squared	Divided	192779	126095	1.52884
125	aquaporin 5. [swissprot;acc:p55064]		Subtracted	71388.5	96035.2	24646.7
	high-mobility group 20a. [refseq;acc:nm_018200]	Ranked	Divided	208.588	171.778	1.21429
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Measured	Subtracted	12471.7	14561.7	2090
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]		Divided	24255.7	18168.9	1.33501
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	Squared		189976	124480	1.52616
	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]	Ranked	Subtracted	285.684	252.234	33.45
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Rooted	Divided	54.8203	67.934	1.23921
	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]		Subtracted	35.6294	49.8119	14.1825
126	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Squared		71387.4	96033.4	24646
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Ranked	Divided	94	114	1.21277
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured		24250	18164.9	1.33499
	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	Ranked	Subtracted	285.684	252.234	33.45
	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted		60.9353	75.094	14.1587
	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]		Divided	60.9342	75.1387	1.23311
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Measured	Subtracted	450.5	2394.5	1944
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	Squared	Divided	189976	124480	1.52616
127	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Ranked	Subtracted	285.684	252.234	33.45
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Squared	Divided	88432.6	58423.3	1.51365
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Rooted	Subtracted	153.191	166.771	13.58
	high-mobility group 20a. [refseq;acc:nm_018200]		Divided	60.9353	75.094	1.23236
	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	Squared	Subtracted	71386.9	96032.5	24645.6
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked	Divided	94	114	1.21277
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Measured	Subtracted	450.5	2394.5	1944
	transcription factor jun-d. [swissprot;acc:p17535]		Divided	5638.2	7523.39	1.33436
128	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Squared	Subtracted	71346.6	95965.1	24618.5
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	Divided	94	114	1.21277
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured		4355.61	5810.82	1.3341
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Rooted	Subtracted	54.6527	67.9743	13.3216
	pnas-18. [sptrembl;acc:q9bzu3]	Squared	Divided	87787.3	58155.8	1.50952
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Ranked	Subtracted	285.684	252.234	33.45
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Measured		11004.2	12944.2	1940
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	Divided	48.0515	39.0445	1.23069
129	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Ranked	Subtracted	285.684	252.234	33.45
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted	Divided	54.2343	66.7323	1.23044
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Measured		4358.13	5811.49	1.33348
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Ranked		94	114	1.21277
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Rooted	Subtracted	54.6625	67.9477	13.2852

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.