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 3258 to 3307 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
408	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Rooted	1	49.9856	45.4432	1.09996
	dok-like protein. [refseq;acc:nm_024872]	Measured	1	6102.59	7081.46	1.1604
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	Measured	0	219.031	227.143	1.03704
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Rooted	0	6.9282	7.14143	1.03078
	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	Squared	1	18995.7	23244.7	1.22368
	seven in absentia homolog 1. [refseq;acc:nm_003031]	Squared	0	14383.6	13569.2	1.06002
	udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	Ranked		9783.63	10111.2	1.03348
409	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Squared		7496.94	7944.03	1.05964
	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Measured	1	6102.59	7081.46	1.1604
	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Measured	0	219.19	227.308	1.03704
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Rooted	0	6.9282	7.14143	1.03078
	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Rooted	1	50.4409	45.8795	1.09942
	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	Ranked		241.045	261.874	1.08641
	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	Squared		18995.6	23242.8	1.22359
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Ranked	0	10598.5	10945.3	1.03272
410	60s ribosomal protein l15. [swissprot;acc:p39030]	Squared	0	1362.84	1286.61	1.05925
	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	Squared	1	19546.1	23881.6	1.22181
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	Measured	1	6102.59	7081.46	1.1604
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]	Measured	0	218.71	226.81	1.03704
	histone h4. [swissprot;acc:p02304]	Ranked		9611.37	9308.99	1.03248
	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Rooted		6.9282	7.14143	1.03078
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Rooted	1	55.5489	50.535	1.09922
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Ranked	1	233.376	253.539	1.0864
411	40s ribosomal protein sa (p40) (34/67 kda laminin receptor) (colon carcinoma laminin-binding protein) (nem/1chd4) (multidrug resistance- associated protein mgr1-ag). [swissprot;acc:p08865]	Squared	0	2967.63	3141.67	1.05865
	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	Ranked		12115.7	12508.3	1.0324
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Rooted		6.9282	7.14143	1.03078
	pp3111 protein. [refseq;acc:nm_022156]	Rooted	1	55.5489	50.535	1.09922
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Squared		17861.2	21821.8	1.22174
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Ranked		233.376	253.539	1.0864
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Measured	0	31122	30022.4	1.03663
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Measured	1	6102.59	7081.46	1.1604
412	5-aminolevulinic acid synthase, nonspecific, mitochondrial precursor (ec 2.3.1.37) (delta-aminolevulinate synthase) (delta-ala synthetase) (alas-h). [swissprot;acc:p13196]	Ranked	0	8546.06	8279.69	1.03217
	60s ribosomal protein l39. [swissprot;acc:p02404]	Measured		3024.78	2923.92	1.03449
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Rooted		6.9282	7.14143	1.03078
	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	Measured	1	3594.31	4169.95	1.16015
	syntaxin 18. [swissprot;acc:q9p2w9]	Rooted		55.5489	50.535	1.09922
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	Squared		19556	23891.8	1.22171
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Squared	0	105483	111123	1.05347
	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	Ranked	1	240.788	261.416	1.08567
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	Ranked		240.913	261.45	1.08525
	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]	Squared		19568.3	23904.6	1.2216
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Squared	0	151156	159204	1.05324
	lifeguard; kiaa0950 protein. [refseq;acc:nm_012306]	Measured		613.385	634.192	1.03392
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Rooted		6.9282	7.14143	1.03078
	protein cgi-147. [swissprot;acc:q9y3e5]	Ranked		5135.25	5298.12	1.03172
	rd protein. [swissprot;acc:p18615]	Rooted	1	55.5489	50.535	1.09922
	vav proto-oncogene. [swissprot;acc:p15498]	Measured		6644.99	7707.8	1.15994
414	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	Measured		6744.05	5815.13	1.15974
	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	Squared		22109.6	26989.4	1.22071
	germ cell-less. [refseq;acc:nm_022471]	Ranked	0	10978.8	10644.4	1.03142

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/