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

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.

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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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 51 to 100 of 77072 in total

Value Type

: Measured
Filtered

: 0

green	red	Network Comparison Type	network_comparison	Interaction Map	Rank	description
0.00001	37	Divided	3700000	Low confidence	22	carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615]
	37		3700000	Low confidence	23	carbohydrate (n-acetylglucosamine-6-o) sulfotransferase 2; carbohydrate (chondroitin 6/keratan) sulfotransferase 2. [refseq;acc:nm_004267]
	60		6000000	High confidence	22	similar to lysozyme c-1 (1,4-beta-n-acylmuramidase c, ec 3.2.1.17). [refseq;acc:nm_032517]
	82		8200000		20	ero1-like. [refseq;acc:nm_014584]
	154		15400000		95	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]
	154		15400000		96	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]
	286		28600000	Low confidence	44	neurogenic locus notch homolog protein 1 precursor (notch 1) (hn1) (translocation-associated notch protein tan-1). [swissprot;acc:p46531]
	286		28600000	Low confidence	45	neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721]
	364		36400000	High confidence	1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
	364		36400000	Low confidence	1
5.56738	199.549		35.8425	High confidence	11	serpin b12. [swissprot;acc:q96p63]
			35.8425	Low confidence	10
		Subtracted	193.982	High confidence	168
		Subtracted	193.982	Low confidence	280
5.71669	199.249	Divided	34.8539	High confidence	12	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]
		Divided	34.8539	Low confidence	11
		Subtracted	193.532	High confidence	169
		Subtracted	193.532	Low confidence	281
6.50325	130.512	Divided	20.0687	High confidence	14	cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]
6.50325	130.512	Subtracted	124.009	High confidence	258
10.6048	383.762	Divided	36.1876	Low confidence	9	ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607]
10.6048	383.762	Subtracted	373.157	Low confidence	166
11.5	14	Divided	1.21739	High confidence	190	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]
		Divided	1.21739	Low confidence	176
		Subtracted	2.5	High confidence	489
		Subtracted	2.5	Low confidence	819
14.3333	19.6667	Divided	1.3721	High confidence	121	4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404]
14.3333	19.6667	Subtracted	5.3334		460
15	1	Divided	15		16	protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]
15	1	Subtracted	14		443
17.5166	0	Subtracted	17.5166	Low confidence	755	jumonji protein. [swissprot;acc:q92833]
17.5166	0.00001	Divided	1751660	Low confidence	5	jumonji protein. [swissprot;acc:q92833]
17.6611	118.878	Divided	6.73106	High confidence	21	syntaxin 10 (syn10). [swissprot;acc:o60499]
17.6611	118.878	Subtracted	101.217		269	syntaxin 10 (syn10). [swissprot;acc:o60499]
18	0	Subtracted	18		428	phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750]
18	0.00001	Divided	1800000		64
19	23		1.21053		195	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]
			1.21053	Low confidence	184
		Subtracted	4	High confidence	464
		Subtracted	4	Low confidence	807
	99	Divided	5.21053		18	camp-regulated phosphoprotein 19 (arpp-19) [contains: camp-regulated phosphoprotein 16 (arpp-16)]. [swissprot;acc:p56211]
	99	Subtracted	80		483
21	44	Divided	2.09524	High confidence	50	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]
21	44	Subtracted	23	High confidence	407
23.6984	48.2534	Divided	2.03615	Low confidence	64	dna helicase homolog (fragment). [sptrembl;acc:q9y645]
23.6984	48.2534	Subtracted	24.555	Low confidence	713	dna helicase homolog (fragment). [sptrembl;acc:q9y645]
26.1599	305.45	Divided	11.6763	High confidence	18	60s ribosomal protein l37a. [swissprot;acc:p12751]
		Divided	11.6763		19	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]
		Subtracted	279.29		114	60s ribosomal protein l37a. [swissprot;acc:p12751]
		Subtracted	279.29		115	25-hydroxyvitamin d-1 alpha hydroxylase, mitochondrial precursor (ec 1.14.-.-) (25-ohd-1 alpha-hydroxylase) (25-hydroxyvitamin d3 1- alpha-hydroxylase) (vd3 1a hydroxylase) (p450c1 alpha) (p450vd1- alpha). [swissprot;acc:o15528]

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/