MK5 Microarray Data

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 2930 to 2979 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
367	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	Squared	Divided	62757.7	50767.8	1.23617
	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Ranked	Subtracted	218.827	238.407	19.58
	dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864]	Measured	Divided	4024.4	4719.35	1.17268
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Ranked		234.146	256.627	1.09601
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Squared	Subtracted	29101.9	35347	6245.1
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	Rooted		60.6732	67.2827	6.6095
	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	Measured		6102.59	7081.46	978.87
368	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Squared		29098.8	35342.6	6243.8
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked		218.827	238.407	19.58
	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]	Squared	Divided	51805.2	41916.4	1.23592
	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	Rooted	Subtracted	63.0663	56.4667	6.5996
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]		Divided	49.5225	54.6817	1.10418
	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Measured		5082.66	5959.99	1.17261
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]		Subtracted	7756.51	8731.76	975.25
	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	Ranked	Divided	242.66	265.715	1.09501
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]			242.159	265.104	1.09475
	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	Measured		3583.56	4194.95	1.17061
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Ranked	Subtracted	239.977	259.525	19.548
	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	Squared	Divided	45960.8	56749.6	1.23474
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Rooted		49.7435	45.0586	1.10397
	nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531]	Measured	Subtracted	7755.69	8730.74	975.05
	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]	Rooted		63.0663	56.4667	6.5996
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Squared		29096	35338.7	6242.7
370	grancalcin. [swissprot;acc:p28676]			29095.7	35338.3	6242.6
	grb2-related adaptor protein. [swissprot;acc:q13588]	Rooted		61.4282	68.0107	6.5825
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Measured	Divided	4108.15	4808.93	1.17058
	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Rooted		49.7435	45.0586	1.10397
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Ranked	Subtracted	218.818	238.358	19.54
	nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392]	Measured		7753.59	8728.13	974.54
	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]	Ranked	Divided	242.159	265.104	1.09475
	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [swissprot;acc:p11171]	Squared		45986	56776.1	1.23464
371	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [swissprot;acc:q9h4g0]			45985.9	56776
	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]		Subtracted	29095.3	35337.6	6242.3
	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Rooted		61.3383	67.8668	6.5285
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Ranked		186.172	166.661	19.511
	pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	Measured		4855.46	5824.52	969.06
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Ranked	Divided	186.52	170.42	1.09447
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	Measured		5067.02	5926.46	1.16961
	zinc finger-like protein 9. [refseq;acc:nm_033414]	Rooted		49.3451	54.4606	1.10367
372	band 4.1-like protein 3 (4.1b) (differentially expressed in adenocarcinoma of the lung protein 1) (dal-1). [swissprot;acc:q9y2j2]	Squared		45986.7	56776.8	1.23464
	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9]	Rooted		49.3451	54.4606	1.10367
	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]		Subtracted	61.3354	67.8623	6.5269
	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Ranked		239.709	259.038	19.329
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Squared		29335.6	35515.5	6179.9
	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	Measured	Divided	5067	5926.17	1.16956
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Ranked		186.52	170.42	1.09447
	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	Measured	Subtracted	4909.79	5878.79	969
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	Ranked	Divided	242.37	265.255	1.09442
	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Squared	Subtracted	28863.2	35031.5	6168.3
	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491]		Divided	45986	56776.1	1.23464

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.