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

Results: HTML CSV LaTeX

Showing element 1673 to 1722 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
210	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Rooted	1	46.8525	53.5316	1.14256
	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Ranked	1	285.684	252.234	1.13261
	mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362]	Ranked	0	17144.8	15405.6	1.11289
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	Squared	1	69549	92953.5	1.33652
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Rooted	0	11.7534	10.3214	1.13874
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Squared		177.23	126.355	1.40264
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Measured		1053.33	887.413	1.18697
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]		1	4068.82	5082.21	1.24906
211	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]		0	2464	2076.5	1.18661
		Rooted	0	48.2208	42.3517	1.13858
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Rooted	1	88.4361	77.5112	1.14095
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Squared	0	98.1677	70.141	1.39958
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Squared	1	14668.3	19547	1.3326
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Ranked	1	285.684	252.234	1.13261
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Ranked	0	10367	9320.25	1.11231
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Measured	1	4068.91	5082.27	1.24905
212	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Rooted		88.4266	77.5047	1.14092
	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Ranked		285.684	252.234	1.13261
	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	Ranked	0	18241.7	16405	1.11196
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Squared	0	98.1677	70.141	1.39958
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Squared	1	14690.3	19560.2	1.3315
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	Measured	1	4446.72	5553.79	1.24896
	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]	Measured	0	2464	2076.5	1.18661
		Rooted		48.2208	42.3517	1.13858
213	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	Measured		1162.21	1376.88	1.18471
	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Rooted	1	105.205	92.2415	1.14054
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Squared	0	98.1677	70.141	1.39958
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Rooted	0	126.359	111.067	1.13768
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	Measured	1	4446.72	5553.79	1.24896
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Ranked	1	210.693	186.95	1.127
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Ranked	0	9379.47	8436.39	1.11179
	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	Squared	1	86861.5	65369.7	1.32877
214	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Ranked	1	191.644	170.192	1.12605
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	Squared	0	98.1677	70.141	1.39958
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Ranked	0	7621.99	8473.85	1.11176
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Rooted	1	105.205	92.2415	1.14054
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Measured	0	13174.7	15605.1	1.18447
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Rooted	0	21.5042	18.9231	1.1364
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Squared	1	52591.3	69845.1	1.32807
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	Measured		4074.83	5086.49	1.24827
215	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Rooted		105.205	92.2415	1.14054
	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	Rooted	0	9.36926	8.24639	1.13617
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Ranked	1	112	126	1.125
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	Squared	0	98.1677	70.141	1.39958
	myosin vi. [swissprot;acc:q9um54]	Ranked	0	10121.5	11250.5	1.11154
	protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723]	Squared	1	86609.4	65234.5	1.32766
	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	Measured	1	16074	12888.4	1.24717
	zinc finger protein 277. [swissprot;acc:q9nrm2]		0	13174.7	15605.1	1.18447
216	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]			12478	14756	1.18256
216	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Rooted		9.36926	8.24639	1.13617

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/