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 Hugo description Network Comparison Type Value Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 725 to 774 of 6456 in total

Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison	
363	SETMAR	set domain and mariner transposase fusion gene. [source:refseq;acc:nm_006515]	Subtracted	233.539	253.197	19.658	
363	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	Divided	231.481	211.131	1.09639	
364	CLEC4M	cd209 antigen-like; putative type ii membrane protein. [source:refseq;acc:nm_014257]	Subtracted	233.539	253.197	19.658	
364	POLR2B	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	Divided	243.208	266.617	1.09625	
365	FCER2	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [source:swissprot;acc:p06734]	Subtracted	233.539	253.197	19.658	
365	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	Divided	242.744	266.07	1.09609	
366	CD209	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [source:refseq;acc:nm_021155]	Subtracted	233.539	253.197	19.658	
366	RPS5	40s ribosomal protein s5. [source:swissprot;acc:p46782]	Divided	242.473	265.756	1.09602	
367	DPP9	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	Subtracted	218.827	238.407	19.58	
367	HNRPM	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	Divided	234.146	256.627	1.09601	
368	DPP8	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	Subtracted	218.827	238.407	19.58	
368	PUS1	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	Divided	242.66	265.715	1.09501	
369	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	Divided	242.159	265.104	1.09475	
369	POLR2E	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [source:swissprot;acc:p19388]	Subtracted	239.977	259.525	19.548	
370	ITGB1BP3	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	Subtracted	218.818	238.358	19.54	
370	NUDT12	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	Divided	242.159	265.104	1.09475	
371	RPS6KC1	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Divided	186.52	170.42	1.09447	
371	SLC15A1	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	Subtracted	186.172	166.661	19.511	
372		ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Divided	186.52	170.42	1.09447	
372	POLR3G	polymerase (rna) iii (dna directed) (32kd). [source:refseq;acc:nm_006467]	Subtracted	239.709	259.038	19.329	
373	DCTN5	dynactin 4. [source:refseq;acc:nm_032486]	Subtracted	233.142	252.253	19.111	
373	MRPL11	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	Divided	242.37	265.255	1.09442	
374	CHRNA7	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	Subtracted	248.152	267.226	19.074	
374	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	Divided	267.208	244.168	1.09436	
375	ADCY6	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	Subtracted	248.152	267.226	19.074	
375	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	Divided	242.686	265.516	1.09407	
376	ADCY5	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [source:swissprot;acc:o95622]	Subtracted	248.152	267.226	19.074	
376	DDX56	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Divided	257.017	234.945	1.09395	
377	LRRC15	leucine-rich repeat-containing protein 15 precursor (hlib). [source:swissprot;acc:q8tf66]	Subtracted	248.152	267.226	19.074	
377	POLR1A	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	Divided	242.691	265.481	1.09391	
378	FEM1B	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	Subtracted	248.152	267.226	19.074	
378	RPL30	60s ribosomal protein l30. [source:swissprot;acc:p04645]	Divided	242.593	265.365	1.09387	
379	AK2	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	Divided	241.509	264.163	1.0938	
379	LRRC3	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	Subtracted	248.152	267.226	19.074	
380		suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	Divided	242.109	264.79	1.09368	
380	LAMC1	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	Subtracted	248.152	267.226	19.074	
381	SLC46A2	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	Subtracted	248.152	267.226	19.074	
381	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	Divided	200.586	183.423	1.09357	
382	DDX54	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Subtracted	253.852	234.808	19.044	
382	TAF7L	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	Divided	200.791	183.66	1.09328	
383	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	Divided	237.862	217.739	1.09242	
383	TRUB1	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	Subtracted	236.245	255.113	18.868	
384		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Subtracted	227.575	208.756	18.819	
384	E2F1	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	Divided	266.421	244.236	1.09083	
385	E2F2	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	Divided	266.421	244.236	1.09083	
385	SNRPF	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Subtracted	227.575	208.756	18.819	
386	RPS14	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	Divided	242.238	264.11	1.09029	
386	RPS9	40s ribosomal protein s9. [source:swissprot;acc:p46781]	Subtracted	238.986	257.784	18.798	
387		40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	Divided	242.238	264.11	1.09029	
387	ATG4A	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Subtracted	56.6768	75.3531	18.6763	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- 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/