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.

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

Results: HTML CSV LaTeX

Showing element 2180 to 2229 of 16578 in total

Value Type  : Ranked
Filtered  : 1

description	Rank	Network Comparison Type	Hugo	Interaction Map	red	network_comparison	green
bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4]	3354	Divided	BRPF3	Low confidence	204.204	1.01554	201.079
bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263]	944	Subtracted	BRD7		205.137	4.91	200.227
	1002	Divided				1.02452
	2747			High confidence	201.477	1.00018	201.514
		Subtracted				0.037
bromodomain containing 8; thyroid hormone receptor coactivating protein; skeletal muscle abundant protein. [refseq;acc:nm_006696]	561		BRD8	Low confidence	206.46	6.185	200.275
	573	Divided				1.03088
bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696]	3139		BRD1	High confidence	0.00001	1	0.00001
		Subtracted			0	0	0
	3298			Low confidence	204.204	3.125	201.079
	3352	Divided				1.01554
bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	2211	Subtracted	BRD2	High confidence	222.96	1.378	224.338
	2241	Divided				1.00618
	3324			Low confidence	197.238	1.01562	194.204
	3390	Subtracted				3.034
bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	2200		BRD3	High confidence	222.965	1.378	224.343
	2237	Divided				1.00618
	3350			Low confidence	197.071	1.01554	194.055
	3404	Subtracted				3.016
bromodomain-containing protein 4 (hunk1 protein). [swissprot;acc:o60885]	2203		BRD4	High confidence	222.959	1.378	224.337
	2238	Divided				1.00618
	3385			Low confidence	197.761	1.01535	194.772
	3445	Subtracted				2.989
bruno-like 4, rna binding protein; rna-binding protein brunol-5; cug-bp and etr-3 like factor 4. [refseq;acc:nm_020180]	1399		BRUNOL4		202.785	4.313	198.472
	1420	Divided				1.02173
bruno-like 5, rna binding protein; rna-binding protein brunol-5; cug-bp and etr-3 like factor 5. [refseq;acc:nm_021938]	1397	Subtracted	BRUNOL5		202.784	4.313	198.471
	1418	Divided				1.02173
bruno-like 6, rna binding protein; rna-binding protein brunol-6. [refseq;acc:nm_052840]	1398	Subtracted	BRUNOL6		202.785	4.313	198.472
	1419	Divided				1.02173
bs4 protein (ny-ren-18 antigen). [swissprot;acc:q9y5a7]	2014	Subtracted	NUB1		203.701	3.837	199.864
	2127	Divided				1.0192
	3214			High confidence	0.00001	1	0.00001
		Subtracted			0	0	0
bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	404		DST		228.463	17.867	246.33
	449	Divided				1.07821
	3419	Subtracted		Low confidence	204.154	3.009	201.145
	3495	Divided				1.01496
bup protein. [refseq;acc:nm_012071]	2911		COMMD3	High confidence	0.00001	1	0.00001
		Subtracted			0	0	0
	4660			Low confidence	208.399	1.226	207.173
	4678	Divided				1.00592
butyrate-induced transcript 1. [refseq;acc:nm_016395]	4133		PTPLAD1		198.355	1.01062	196.271
	4177	Subtracted				2.084
bystin. [swissprot;acc:q13895]	1050		BYSL	High confidence	239.505	6.32	233.185
	1149	Divided				1.0271
	2694			Low confidence	200.546	1.01757	197.084
	2699	Subtracted				3.462
c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586]	1487		MTHFD1		203.321	4.228	199.093
	1541	Divided				1.02124
	1718	Subtracted		High confidence	228.932	2.8	231.732

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
- Hugo is the HGNC identifier if it exists
- 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.