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 Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2951 to 3000 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
369	ras-related c3 botulinum toxin substrate 3 (p21-rac3). [source:swissprot;acc:o14658]	Squared	0	346.699	309.317	1.12085	
369	uncharacterized bone marrow protein bm033. [source:refseq;acc:nm_018452]	Rooted	0	17.8274	17.1002	1.04253	
370	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [source:swissprot;acc:o75832]	Rooted	0	30.7424	32.0298	1.04188	
370	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [source:refseq;acc:nm_032959]	Measured	0	1049.21	989.438	1.06041	
370	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Measured	1	4108.15	4808.93	1.17058	
370	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [source:swissprot;acc:p50579]	Rooted	1	49.7435	45.0586	1.10397	
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Ranked	1	242.159	265.104	1.09475	
370	protein 4.1 (band 4.1) (p4.1) (epb4.1) (4.1r). [source:swissprot;acc:p11171]	Squared	1	45986	56776.1	1.23464	
370	pyruvate dehydrogenase e1 component alpha subunit, testis-specific form, mitochondrial precursor (ec 1.2.4.1) (pdhe1-a type ii). [source:swissprot;acc:p29803]	Ranked	0	13652.7	13061	1.0453	
370	survival motor neuron protein (component of gems 1) (gemin1). [source:swissprot;acc:q16637]	Squared	0	1039.56	927.649	1.12064	
371	band 4.1-like protein 1 (neuronal protein 4.1) (4.1n). [source:swissprot;acc:q9h4g0]	Squared	1	45985.9	56776	1.23464	
371	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [source:sptrembl;acc:q9h5a9]	Squared	0	18585	20796.3	1.11898	
371	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [source:swissprot;acc:q9nry6]	Measured	0	1631.97	1542.23	1.05819	
371	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [source:swissprot;acc:p07237]	Rooted	0	20.9428	21.8063	1.04123	
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Ranked	1	186.52	170.42	1.09447	
371	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	Measured	1	5067.02	5926.46	1.16961	
371	swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [source:refseq;acc:nm_003075]	Ranked	0	13247.9	12674.2	1.04527	
371	zinc finger-like protein 9. [source:refseq;acc:nm_033414]	Rooted	1	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). [source:swissprot;acc:q9y2j2]	Squared	1	45986.7	56776.8	1.23464	
372	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [source:swissprot;acc:p35606]	Measured	0	5427.25	5130.58	1.05782	
372	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Ranked	0	11869.9	12402.7	1.04489	
372	enigma protein; lim domain protein. [source:refseq;acc:nm_005451]	Squared	0	21.836	19.5177	1.11878	
372	membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [source:swissprot;acc:q9umx9]	Rooted	1	49.3451	54.4606	1.10367	
372	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Measured	1	5067	5926.17	1.16956	
372	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Ranked	1	186.52	170.42	1.09447	
372	secreted modular calcium-binding protein 1. [source:refseq;acc:nm_022137]	Rooted	0	11.9476	12.4394	1.04116	
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Ranked	1	242.37	265.255	1.09442	
373	band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [source:swissprot;acc:o43491]	Squared	1	45986	56776.1	1.23464	
373	guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [source:swissprot;acc:p36915]	Rooted	1	49.3451	54.4606	1.10367	
373	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [source:swissprot;acc:q16719]	Measured	0	2713.5	2864.68	1.05571	
373	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [source:swissprot;acc:q99683]	Ranked	0	10598.2	11061.5	1.04371	
373	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	Measured	1	5066.99	5926.1	1.16955	
373	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	Rooted	0	30.3054	31.5389	1.0407	
373	sprouty homolog 4 (spry-4). [source:swissprot;acc:q9c004]	Squared	0	215.107	192.635	1.11666	
374	60s ribosomal protein l26. [source:swissprot;acc:q02877]	Rooted	1	50.2549	45.5599	1.10305	
374	adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [source:swissprot;acc:p07741]	Measured	0	2323.8	2452.23	1.05527	
374	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [source:swissprot;acc:p24298]	Squared	0	2572.14	2869.96	1.11579	
374	calcyphosine. [source:swissprot;acc:q13938]	Ranked	0	9874.54	9478.1	1.04183	
374	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [source:refseq;acc:nm_032260]	Rooted	0	30.2858	31.5117	1.04048	
374	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Measured	1	5066.93	5925.38	1.16942	
374	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [source:swissprot;acc:q9nrc6]	Squared	1	45987	56777.1	1.23463	
374	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Ranked	1	267.208	244.168	1.09436	
375	45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [source:swissprot;acc:q9brk5]	Squared	1	45987	56777.1	1.23463	
375	60s ribosomal protein l35. [source:swissprot;acc:p42766]	Rooted	1	50.2545	45.5637	1.10295	
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	Ranked	1	242.686	265.516	1.09407	
375	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [source:swissprot;acc:p14061]	Measured	0	2323.8	2452.23	1.05527	
375	germ cell-less. [source:refseq;acc:nm_022471]	Rooted	0	27.8491	26.7806	1.0399	
375	importin 9. [source:refseq;acc:nm_018085]	Squared	0	1062.18	952.74	1.11487	
375	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. [source:refseq;acc:nm_015975]	Ranked	0	14247.6	13686.9	1.04097	
375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	Measured	1	4700.42	5492.63	1.16854	

Legend:
- Rank is the rank after comparing the two networks
- 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/