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 3558 to 3607 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
445	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Squared	0	99229.9	96418.4	1.02916
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Rooted	1	50.1635	45.7274	1.09701
	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]	Squared	1	58831	48584.2	1.21091
446	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	Rooted	0	22.2195	22.7215	1.02259
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Ranked	0	7965.06	7790.78	1.02237
	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	Rooted	1	54.9019	60.2111	1.0967
	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	Ranked	1	224.049	207.785	1.07827
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Squared	0	7089.15	7292.72	1.02872
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Measured	0	1549.26	1522.06	1.01787
	nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366]	Measured	1	3766.03	4329.37	1.14958
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Squared	1	29335.6	35515.5	1.21066
447	40s ribosomal protein s3a. [swissprot;acc:p49241]	Measured	0	2929.51	2879.55	1.01735
	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Rooted	0	32.2451	32.9629	1.02226
	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	Rooted	1	54.9019	60.2111	1.0967
	histone h2b. [refseq;acc:nm_175055]	Squared	0	7090.75	7294.29	1.02871
	pescadillo homolog 1. [swissprot;acc:o00541]	Measured	1	3751.14	4310.89	1.14922
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked	0	12532.2	12808.8	1.02207
	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955]	Ranked	1	224.049	207.785	1.07827
	sipl protein. [refseq;acc:nm_018269]	Squared		30155.1	36495	1.21024
448	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]			20350.3	16816.1	1.21017
	histone h2b.s (h2b/s). [swissprot;acc:p57053]		0	7090.47	7294.01	1.02871
	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Ranked	1	228.468	246.338	1.07822
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Measured	1	6259.3	7190.91	1.14884
	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	Ranked	0	2939	2876	1.02191
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Measured	0	524.415	533.236	1.01682
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Rooted	1	50.1671	45.7563	1.0964
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Rooted	0	19.2553	19.676	1.02185
449	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	Ranked	0	9897.12	9690.83	1.02129
	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	Ranked	1	228.463	246.33	1.07821
	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	Squared		20348.5	16817.2	1.20998
	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Rooted		50.162	45.7659	1.09606
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Squared	0	7089.47	7293.03	1.02871
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Measured		5699.32	5607.7	1.01634
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	Rooted		17.104	16.765	1.02022
	wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7]	Measured	1	3761.59	4319.69	1.14837
450	acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]	Squared	1	31646.1	38288.7	1.2099
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Measured	0	4158.33	4094.09	1.01569
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Squared	0	7091.16	7294.68	1.0287
	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	Measured	1	4889.21	5610.52	1.14753
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Rooted	0	41.788	42.5828	1.01902
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Ranked	1	235.94	218.837	1.07815
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Ranked	0	11290.8	11525.8	1.02081
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Rooted	1	50.4595	46.0411	1.09597
451	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Measured	0	2683.61	2642.79	1.01545
	60s ribosomal protein l39. [swissprot;acc:p02404]	Rooted		34.7116	35.3591	1.01865
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Ranked		14010.2	13737.2	1.01987
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Squared		7090.8	7294.33	1.0287
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Rooted	1	50.268	45.8663	1.09597
	n-myc proto-oncogene protein. [swissprot;acc:p04198]	Measured		4889.71	5610.69	1.14745
	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	Ranked		239.092	257.705	1.07785

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/