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 description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3101 to 3150 of 14920 in total 
Interaction Map	High confidence
Network Comparison Type	Divided

Rank	description	Value Type	Filtered	red	green	network_comparison	
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [source:refseq;acc:nm_138574]	Measured	1	4533.74	5279.4	1.16447	
388	scratch; scratch 1. [source:refseq;acc:nm_031309]	Measured	0	1398.21	1339.9	1.04352	
388	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	Rooted	1	50.3345	45.6718	1.10209	
388	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	Ranked	1	227.575	208.756	1.09015	
389	60s ribosomal protein l34. [source:swissprot;acc:p49207]	Rooted	1	50.3345	45.6718	1.10209	
389	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	Squared	1	31819.7	39222.2	1.23264	
389	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	Ranked	0	11794.7	11375.4	1.03686	
389	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	Measured	0	11512.3	12011.7	1.04338	
389	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [source:swissprot;acc:q9nzm3]	Rooted	0	30.454	29.4181	1.03521	
389	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Squared	0	605.501	557.57	1.08596	
389	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	Measured	1	4533.74	5279.4	1.16447	
389	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	Ranked	1	227.575	208.756	1.09015	
390	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	Ranked	1	241.828	263.62	1.09011	
390	alpha-nac protein. [source:sptrembl;acc:q9h009]	Ranked	0	14204.4	14724.5	1.03662	
390	alpha-nac protein. [source:sptrembl;acc:q9h009]	Squared	0	12.1126	13.1421	1.08499	
390	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	Measured	0	11512.3	12011.7	1.04338	
390	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	Squared	1	28895.6	35572.8	1.23108	
390	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	Rooted	1	50.3345	45.6718	1.10209	
390	rw1 protein (fragment). [source:swissprot;acc:q92545]	Measured	1	4533.74	5279.4	1.16447	
390	williams-beuren syndrome critical region protein 20 copy b. [source:refseq;acc:nm_145645]	Rooted	0	7.21166	7.46223	1.03475	
391	40s ribosomal protein s16. [source:swissprot;acc:p17008]	Ranked	1	241.828	263.62	1.09011	
391	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [source:swissprot;acc:q14974]	Squared	1	28895.6	35572.8	1.23108	
391	nascent-polypeptide-associated complex alpha polypeptide. [source:refseq;acc:nm_005594]	Ranked	0	14223.9	14738.5	1.03618	
391	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	Squared	0	9106.26	9878.65	1.08482	
391	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	Rooted	1	50.3345	45.6718	1.10209	
391	seven in absentia homolog 1. [source:refseq;acc:nm_003031]	Measured	0	2221.04	2316.94	1.04318	
391	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	Measured	1	3658.76	3144.39	1.16358	
391	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [source:refseq;acc:nm_018044]	Rooted	0	7.21166	7.46223	1.03475	
392	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	Ranked	1	241.83	263.615	1.09008	
392	60s ribosomal protein l14 (cag-isl 7). [source:swissprot;acc:p50914]	Measured	0	229.211	219.891	1.04238	
392	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	Rooted	1	50.3313	45.6913	1.10155	
392	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	Measured	1	3641.89	4236.95	1.16339	
392	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]	Squared	0	94.678	87.5656	1.08122	
392	seven in absentia homolog 1. [source:refseq;acc:nm_003031]	Ranked	0	9854.67	10201.4	1.03518	
392	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	Squared	1	28895.6	35572.8	1.23108	
392	williams beuren syndrome chromosome region 20c isoform 1. [source:refseq;acc:nm_032158]	Rooted	0	7.21166	7.46223	1.03475	
393	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	Squared	0	9.11845	8.43969	1.08042	
393	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	Rooted	1	49.8842	45.2875	1.1015	
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	Measured	1	4490.28	5222.25	1.16301	
393	histone h2b.q (h2b/q) (h2b-gl105). [source:swissprot;acc:q16778]	Measured	0	2131.42	2218.51	1.04086	
393	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	Rooted	0	33.8811	32.7487	1.03458	
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Ranked	1	225.719	207.072	1.09005	
393	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	Ranked	0	12576	13010	1.03451	
393	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	Squared	1	28895.6	35572.8	1.23108	
394	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Ranked	0	10196.9	9857.79	1.0344	
394	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). [source:swissprot;acc:q9y6q5]	Squared	0	70.823	65.5835	1.07989	
394	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	Measured	1	4490.28	5222.25	1.16301	
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	Ranked	1	218.827	238.407	1.08948	
394	histone h2b.d (h2b/d). [source:swissprot;acc:q99877]	Measured	0	2131.52	2218.58	1.04084	
394	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Squared	1	17248.4	21214	1.22991	

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/