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

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 1551 to 1600 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
97	septin 10 isoform 1. [refseq;acc:nm_144710]	Measured	Subtracted	1	16067.4	19094.4	3027
	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	Ranked		0	11522.8	13684.9	2162.1
98	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Rooted			83.9673	88.8829	4.9156
	brain protein 44. [swissprot;acc:o95563]	Measured		1	15999.1	19007.1	3008
	guanine nucleotide-binding protein g(k), alpha subunit (g(i) alpha-3). [swissprot;acc:p08754]	Rooted			40.2797	24.3705	15.9092
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Measured		0	39165	39485	320
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Ranked	Divided	1	88.2482	110.265	1.24949
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Squared	Subtracted	0	310884	312261	1377
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Ranked	Divided		7234.6	8858.94	1.22452
	pp3111 protein. [refseq;acc:nm_022156]	Measured			789	530	1.48868
		Squared			147.342	66.4852	2.21616
	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	Measured		1	2353.63	3225.65	1.3705
	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100]	Ranked	Subtracted		204.641	160.957	43.684
	septin 10 isoform 1. [refseq;acc:nm_144710]	Squared			89578.7	125883	36304.3
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Rooted	Divided	0	13.2903	17.4395	1.3122
	transcription factor lbx1. [swissprot;acc:p52954]			1	47.6504	36.9304	1.29028
	trs85 homolog. [swissprot;acc:q9y2l5]	Squared			227160	146079	1.55505
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	Ranked	Subtracted	0	11520.7	13680.4	2159.7
99	brain protein 44. [swissprot;acc:o95563]	Squared		1	89182.8	125229	36046.2
	dystrophin. [swissprot;acc:p11532]	Measured		0	427.217	111.739	315.478
	jun dimerization protein. [refseq;acc:nm_130469]	Ranked		1	204.641	160.957	43.684
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]		Divided		88.2482	110.265	1.24949
	mosaic protein lgn. [swissprot;acc:p81274]	Rooted			47.6504	36.9304	1.29028
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Ranked		0	12787.8	10454.7	1.22316
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Rooted	Subtracted		27.8028	22.9122	4.8906
	putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	Squared	Divided		492.157	225.924	2.17842
	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	Ranked	Subtracted		7584.72	9706.12	2121.4
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Rooted	Divided		31.495	24.0263	1.31086
	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]	Measured		1	2353.63	3225.65	1.3705
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]		Subtracted		15999.1	19007.1	3008
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Rooted			19.9625	35.798	15.8355
	transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]	Measured	Divided	0	817.81	551.434	1.48306
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Squared	Subtracted		19277.3	20652.4	1375.1
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]		Divided	1	226186	145568	1.55382
100	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Measured		0	594	402	1.47761
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	Rooted	Subtracted		22.4608	17.665	4.7958
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	Squared	Divided	1	226186	145568	1.55382
	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Ranked		0	9183.49	11217.7	1.22151
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	Measured	Subtracted		2698.62	3010.22	311.6
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Ranked			12584.5	10470.6	2113.9
	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]	Measured	Divided	1	2353.63	3225.65	1.3705
	fos-related antigen 2. [swissprot;acc:p15408]	Ranked	Subtracted		204.641	161.046	43.595
	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	Rooted	Divided	0	20.0501	15.3244	1.30838
	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	Squared	Subtracted		310373	311745	1372
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Ranked	Divided	1	88.2482	110.265	1.24949
	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]	Squared		0	492.157	225.924	2.17842
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	Rooted		1	47.6504	36.9304	1.29028
	septin 6. [swissprot;acc:q14141]	Measured	Subtracted		15959.9	18957.1	2997.2
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Squared			89182.8	125229	36046.2
	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Rooted			19.9625	35.798	15.8355

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.