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	Filtered	Interaction Map	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 101 to 150 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
7	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Rooted	Divided	0	0.00001	9.43398	943398
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Ranked	Subtracted		22286	13216	9070
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared		1	310840	442993	132153
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Rooted			145.551	168.796	23.245
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Ranked			288.754	212.554	76.2
	sedlin. [swissprot;acc:o14582]	Measured	Divided	0	0.00001	43	4300000
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Squared	Subtracted		82802.3	111762	28959.7
	sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906]	Measured	Divided	1	1153.5	339.5	3.39764
		Squared			314.926	27.2805	11.544
		Rooted			33.9632	18.4255	1.84327
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]		Subtracted	0	65.4535	49.8523	15.6012
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Measured			13174.7	15605.1	2430.4
8	db83 protein. [swissprot;acc:p57088]		Divided	1	1153.5	339.5	3.39764
		Squared			314.926	27.2805	11.544
		Rooted			33.9632	18.4255	1.84327
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	Subtracted		250303	354894	104591
	ero1-like. [refseq;acc:nm_014584]		Divided	0	1.59148	0.00001	159148
		Rooted			9.05539		905539
	hbs1-like. [refseq;acc:nm_006620]	Ranked		1	215	322	1.49767
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]		Subtracted	0	22286	13216	9070
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]			1	288	362	74
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Rooted		0	72.1137	56.7758	15.3379
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Ranked	Divided		11525	21888	1.89918
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Measured	Subtracted		5106.93	7500.75	2393.82
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]			1	21185	28492	7307
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted			145.551	168.796	23.245
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Measured	Divided	0	0.00001	43	4300000
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Squared	Subtracted		414704	386144	28560
9	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]				195397	170319	25078
	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	Measured			12478	14756	2278
	ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]		Divided		85	6410	75.4118
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Ranked	Subtracted		22286	13216	9070
	junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]			1	288	362	74
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted			145.551	168.796	23.245
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]			0	126.359	111.067	15.292
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Measured		1	21185	28492	7307
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Squared			256169	162517	93652
	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]		Divided	0	0.852071	0.00001	85207.1
		Rooted			7.74597		774597
	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Measured		1	398.5	1281.5	3.21581
		Squared			37.5863	388.696	10.3414
		Rooted			19.9625	35.798	1.79326
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Ranked		0	11525	21888	1.89918
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]			1	212	309	1.45755
10	baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	Squared	Subtracted	0	176989	155919	21070
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Ranked	Divided		7509.39	14178.1	1.88805
		Rooted	Subtracted		54.2583	40.2058	14.0525
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Squared	Divided		0.00001	0.823905	82390.5
		Rooted				7.68115	768115
	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]	Measured			85	6410	75.4118

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.