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.

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 101 to 150 of 29840 in total

Interaction Map  : High confidence

Rank	Value Type	description	Network Comparison Type	Filtered	green	red	network_comparison
7	Ranked	cab2. [refseq;acc:nm_033419]	Divided	0	10950	21866	1.99689
		homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]		1	322	215	1.49767
		homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Subtracted	0	13216	22286	9070
		protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]		1	212.554	288.754	76.2
	Squared	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Divided	0	1.87479	0.00001	187479
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Subtracted	1	442993	310840	132153
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]		0	111762	82802.3	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]	Divided	1	27.2805	314.926	11.544
	Rooted	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		0	9.43398	0.00001	943398
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Subtracted	1	168.796	145.551	23.245
		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]	Divided		18.4255	33.9632	1.84327
		ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Subtracted	0	49.8523	65.4535	15.6012
8	Measured	db83 protein. [swissprot;acc:p57088]	Divided	1	339.5	1153.5	3.39764
		nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Subtracted	0	7500.75	5106.93	2393.82
		pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]		1	28492	21185	7307
		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Divided	0	43	0.00001	4300000
	Ranked	hbs1-like. [refseq;acc:nm_006620]		1	322	215	1.49767
		homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	0	13216	22286	9070
		junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]		1	362	288	74
		nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided	0	21888	11525	1.89918
	Squared	db83 protein. [swissprot;acc:p57088]		1	27.2805	314.926	11.544
		deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Subtracted		354894	250303	104591
		ero1-like. [refseq;acc:nm_014584]	Divided	0	0.00001	1.59148	159148
		transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Subtracted		386144	414704	28560
	Rooted	db83 protein. [swissprot;acc:p57088]	Divided	1	18.4255	33.9632	1.84327
		ero1-like. [refseq;acc:nm_014584]		0	0.00001	9.05539	905539
		nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Subtracted		56.7758	72.1137	15.3379
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		1	168.796	145.551	23.245
9	Measured	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]		0	14756	12478	2278
		ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	Divided		6410	85	75.4118
		pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	Subtracted	1	28492	21185	7307
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Divided		1281.5	398.5	3.21581
	Ranked	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Subtracted	0	13216	22286	9070
		junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39]		1	362	288	74
		transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Divided	0	21888	11525	1.89918
		xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]		1	309	212	1.45755
	Squared	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Subtracted	0	170319	195397	25078
		protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]		1	162517	256169	93652
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Divided	0	0.00001	0.852071	85207.1
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		1	388.696	37.5863	10.3414
	Rooted	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Subtracted		168.796	145.551	23.245
		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		0	111.067	126.359	15.292
		similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]	Divided		0.00001	7.74597	774597
		tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]		1	35.798	19.9625	1.79326
10	Measured	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851]		0	6410	85	75.4118
		myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Subtracted		6193.07	7830.62	1637.55
		pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]		1	28492	21185	7307
		tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	Divided		1281.5	398.5	3.21581
	Ranked	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]		0	14178.1	7509.39	1.88805
		protein x 0004. [refseq;acc:nm_016301]		1	309	212	1.45755

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.