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.

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

Legend:
- Rank is the rank after comparing the two networks
- 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/