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

Results: HTML CSV LaTeX

Showing element 3180 to 3229 of 29840 in total

Interaction Map

: High confidence

Rank	Value Type	description	Network Comparison Type	Filtered	red	green	network_comparison
199	Squared	thymus-specific serine protease precursor (ec 3.4.-.-). [swissprot;acc:q9nqe7]	Divided	1	71062.2	95488.6	1.34373
	Rooted	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Divided	0	23.8722	20.9331	1.1404
		luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Subtracted	1	55.297	65.9236	10.6266
		source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Divided	1	61.2893	70.3856	1.14842
		tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677]	Subtracted	0	10.9527	8.13999	2.81271
200	Measured	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	Subtracted	1	10635.3	12111.4	1476.1
		crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	Divided	1	4808.79	6074.21	1.26315
		dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Divided	0	578.056	482.7	1.19755
		glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210]	Subtracted	0	1705.19	1547.2	157.99
	Ranked	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Subtracted	1	241.808	267.335	25.527
		egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Divided	1	242.718	276.018	1.1372
		peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Divided	0	8786.74	7870.3	1.11644
		transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Subtracted	0	13483.3	14685.4	1202.1
	Squared	gk001 protein. [refseq;acc:nm_020198]	Divided	1	71062.2	95488.6	1.34373
		mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Subtracted	1	42411.6	55802.1	13390.5
		muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Subtracted	0	129.158	488.851	359.693
		transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Divided		5317.39	3738.08	1.42249
	Rooted	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]			23.8722	20.9333	1.14039
		oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]		1	61.2893	70.3856	1.14842
		serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Subtracted	1	63.5827	53.0856	10.4971
		syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]		0	11.5003	8.68906	2.81124
201	Measured	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]			6699.82	6856.28	156.46
		swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	Divided		6804.88	5690.63	1.1958
		t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Divided	1	4810.22	6075.04	1.26294
		translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571]	Subtracted		10603.5	12069.5	1466
	Ranked	60s ribosomal protein l11. [swissprot;acc:p39026]			241.828	267.346	25.518
		alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]		0	6814	8009	1195
		maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	Divided	0	16853	15123	1.1144
		splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]		1	240.133	211.382	1.13601
	Squared	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		0	351.996	499.177	1.41813
		calsyntenin-2 precursor. [swissprot;acc:q9h4d0]		1	71033.4	95440.2	1.3436
		deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Subtracted	0	468.221	113.017	355.204
		mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]		1	42411.6	55802.1	13390.5
	Rooted	chromodomain y-like protein 2. [refseq;acc:nm_152342]		0	33.0227	30.2263	2.7964
		cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]		1	138.375	127.926	10.449
		dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Divided	1	61.2893	70.3856	1.14842
		keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Divided	0	23.8722	20.9336	1.14038
202	Measured	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Subtracted	0	2039.07	2194.52	155.45
		calsyntenin-1 precursor. [swissprot;acc:o94985]	Subtracted	1	10603.5	12069.5	1466
		crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	Divided	0	606.049	723.75	1.19421
		enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	Divided	1	4812.01	6076.09	1.26269
	Ranked	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	Subtracted	1	240.758	266.079	25.321
		serpin b11. [swissprot;acc:q96p15]	Divided	0	16853	15123	1.1144
		short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	Divided	1	201.478	228.784	1.13553
		voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Subtracted	0	8214.41	7026.41	1188
	Squared	calsyntenin-3 precursor. [swissprot;acc:q9bqt9]	Divided	1	71030.1	95434.8	1.34358
		dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Divided	0	3339.18	2360.97	1.41433
		neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Subtracted	1	42411.6	55802.1	13390.5
		transducin beta-like 2 protein (ws beta-transducin repeats protein) (ws-betatrp) (williams-beuren syndrome chromosome region 13 protein). [swissprot;acc:q9y4p3]		0	631.532	280.389	351.143
	Rooted	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]		0	10.9038	8.12243	2.78137

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/