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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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 1010 to 1059 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
127	high-mobility group 20a. [refseq;acc:nm_018200]	Rooted	1	60.9353	75.094	1.23236
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Measured	0	86	64	1.34375
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Ranked	1	94	114	1.21277
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Rooted	0	37.9737	31.257	1.21489
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Squared		799.337	432.882	1.84655
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Ranked		9411.34	11119.7	1.18152
	transcription factor jun-d. [swissprot;acc:p17535]	Measured	1	5638.2	7523.39	1.33436
128	60s ribosomal protein l39. [swissprot;acc:p02404]	Ranked	0	11564.4	9794.29	1.18073
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Ranked	1	94	114	1.21277
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Squared	0	166.774	90.363	1.8456
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Measured	1	4355.61	5810.82	1.3341
	mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650]	Measured	0	81.504	60.8613	1.33918
	phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669]	Rooted	0	37.9737	31.257	1.21489
	pnas-18. [sptrembl;acc:q9bzu3]	Squared	1	87787.3	58155.8	1.50952
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Rooted	1	48.0515	39.0445	1.23069
129	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Squared	0	21723.1	39570.4	1.82158
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Rooted	1	54.2343	66.7323	1.23044
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Ranked	0	14222.5	12058.6	1.17945
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Measured	1	4358.13	5811.49	1.33348
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Ranked	1	94	114	1.21277
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Rooted	0	27.8028	22.9122	1.21345
	pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	Squared	1	178263	118639	1.50257
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured	0	606.485	454.837	1.33341
130	44050 protein. [refseq;acc:nm_178832]	Squared	1	148058	99628.4	1.4861
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Squared	0	21165.1	38499.2	1.81899
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Ranked	0	14476.2	17069.5	1.17914
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Measured	1	2234.68	2978.53	1.33287
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted	1	55.1026	67.5701	1.22626
	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Measured	0	42	56	1.33333
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked	1	94	114	1.21277
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Rooted	0	12.7347	10.4997	1.21286
131	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Rooted		19.3128	16.0484	1.20341
	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	Ranked		8375.43	9873.58	1.17887
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Measured	1	2234.73	2978.57	1.33285
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Rooted		55.1113	67.5537	1.22577
	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	Squared		148058	99628.4	1.4861
	serpin b11. [swissprot;acc:q96p15]	Measured	0	42	56	1.33333
	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]	Ranked	1	294.053	242.562	1.21228
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Squared	0	451.156	817.981	1.81308
132	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Squared	1	36359.2	24466.8	1.48606
	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Rooted	0	23.9003	19.8655	1.20311
	cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	Measured	0	42	56	1.33333
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Measured	1	2236.61	2980.35	1.33253
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	Rooted	1	44.963	55.0576	1.22451
	lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428]	Squared	0	1.75053	0.969467	1.80566
	rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372]	Ranked	0	19048	22389	1.1754
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		1	350	290	1.2069
133	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]		0	6814	8009	1.17537
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Measured	0	252	335	1.32937
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Measured	1	23421.5	17580.4	1.33225

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/