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 - 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.

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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 6258 to 6307 of 29840 in total

Interaction Map

: High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
392	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Measured	Divided	0	229.211	219.891	1.04238
	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Rooted		1	50.3313	45.6913	1.10155
	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	Measured			3641.89	4236.95	1.16339
	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	Measured	Subtracted		6251.91	7192.08	940.17
	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Squared		0	61.898	74.2593	12.3613
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	Squared		1	26157.6	20236.2	5921.4
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]	Measured		0	6428	6396.8	31.2
	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	Ranked		1	239.092	257.705	18.613
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Squared	Divided	0	94.678	87.5656	1.08122
	ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	Rooted	Subtracted		8.05424	8.90701	0.85277
	seven in absentia homolog 1. [refseq;acc:nm_003031]	Ranked	Divided		9854.67	10201.4	1.03518
	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	Ranked	Subtracted		10303.7	10687.4	383.7
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	Squared	Divided	1	28895.6	35572.8	1.23108
	vav-3 protein. [swissprot;acc:q9ukw4]	Rooted	Subtracted	1	66.089	72.3555	6.2665
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	Rooted	Divided	0	7.21166	7.46223	1.03475
393	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]	Squared	Subtracted	1	26157.6	20236.2	5921.4
	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Squared	Divided	0	9.11845	8.43969	1.08042
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Rooted	Divided	1	49.8842	45.2875	1.1015
	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	Ranked	Subtracted		238.921	257.327	18.406
	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	Measured	Divided		4490.28	5222.25	1.16301
	grancalcin. [swissprot;acc:p28676]		Subtracted		6251.96	7192.13	940.17
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]		Divided	0	2131.42	2218.51	1.04086
	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	Rooted	Subtracted		8.05424	8.90701	0.85277
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Squared			15.4957	3.83288	11.6628
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Measured			3855.78	3825.73	30.05
		Rooted	Divided		33.8811	32.7487	1.03458
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Ranked		1	225.719	207.072	1.09005
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Ranked		0	12576	13010	1.03451
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared		1	28895.6	35572.8	1.23108
	vav-2 protein. [swissprot;acc:p52735]	Rooted	Subtracted	1	66.088	72.2597	6.1717
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	Ranked	Subtracted	0	5540	5921	381
394	60s ribosomal protein l12. [swissprot;acc:p30050]	Ranked	Divided		10196.9	9857.79	1.0344
	adaptor-related protein complex 1, mu 2 subunit (mu-adaptin 2) (adaptor protein complex ap-1 mu-2 subunit) (golgi adaptor ha1/ap1 adaptin mu-2 subunit) (clathrin assembly protein assembly protein complex 1 medium chain 2) (ap-mu chain family member mu1b). [swissprot;acc:q9y6q5]	Squared	Divided		70.823	65.5835	1.07989
	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	Squared	Subtracted	1	26157.6	20236.2	5921.4
	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	Measured	Divided	1	4490.28	5222.25	1.16301
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Squared	Subtracted	0	15.0305	26.5621	11.5316
	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	Ranked	Subtracted	1	207.889	226.226	18.337
	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Ranked	Divided		218.827	238.407	1.08948
	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	Rooted	Subtracted		58.0752	64.23	6.1548
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Rooted		0	62.6706	61.8357	0.8349
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-4 subunit. [swissprot;acc:p50150]	Measured		1	1834.33	895.134	939.196
	histone h2b.d (h2b/d). [swissprot;acc:q99877]		Divided	0	2131.52	2218.58	1.04084
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]		Subtracted	0	3889.5	3919.25	29.75
	mad protein (max dimerizer). [swissprot;acc:q05195]	Squared	Divided	1	17248.4	21214	1.22991
	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Rooted		1	58.6533	64.5958	1.10132
	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	Rooted		0	13.4343	13.8963	1.03439
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	Ranked	Subtracted		20875	20495	380
395	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	Ranked	Subtracted		9566.15	9936.37	370.22
		Rooted	Divided		32.0326	30.9731	1.03421
	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	Squared	Subtracted		202.436	212.386	9.95

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/