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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 3101 to 3150 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Measured	1	4533.74	5279.4	1.16447
	scratch; scratch 1. [refseq;acc:nm_031309]	Measured	0	1398.21	1339.9	1.04352
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Rooted	1	50.3345	45.6718	1.10209
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Ranked		227.575	208.756	1.09015
389	60s ribosomal protein l34. [swissprot;acc:p49207]	Rooted		50.3345	45.6718	1.10209
	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	Squared		31819.7	39222.2	1.23264
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Ranked	0	11794.7	11375.4	1.03686
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Measured		11512.3	12011.7	1.04338
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Rooted		30.454	29.4181	1.03521
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Squared		605.501	557.57	1.08596
	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Measured	1	4533.74	5279.4	1.16447
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Ranked		227.575	208.756	1.09015
390	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]			241.828	263.62	1.09011
	alpha-nac protein. [sptrembl;acc:q9h009]		0	14204.4	14724.5	1.03662
	alpha-nac protein. [sptrembl;acc:q9h009]	Squared		12.1126	13.1421	1.08499
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Measured		11512.3	12011.7	1.04338
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	1	28895.6	35572.8	1.23108
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Rooted		50.3345	45.6718	1.10209
	rw1 protein (fragment). [swissprot;acc:q92545]	Measured		4533.74	5279.4	1.16447
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Rooted	0	7.21166	7.46223	1.03475
391	40s ribosomal protein s16. [swissprot;acc:p17008]	Ranked	1	241.828	263.62	1.09011
	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	Squared	1	28895.6	35572.8	1.23108
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Ranked	0	14223.9	14738.5	1.03618
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Squared	0	9106.26	9878.65	1.08482
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Rooted	1	50.3345	45.6718	1.10209
	seven in absentia homolog 1. [refseq;acc:nm_003031]	Measured	0	2221.04	2316.94	1.04318
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Measured	1	3658.76	3144.39	1.16358
	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. [refseq;acc:nm_018044]	Rooted	0	7.21166	7.46223	1.03475
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	Ranked	1	241.83	263.615	1.09008
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Measured	0	229.211	219.891	1.04238
	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Rooted	1	50.3313	45.6913	1.10155
	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	Measured	1	3641.89	4236.95	1.16339
	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	Squared	0	94.678	87.5656	1.08122
	seven in absentia homolog 1. [refseq;acc:nm_003031]	Ranked	0	9854.67	10201.4	1.03518
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	Squared	1	28895.6	35572.8	1.23108
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	Rooted	0	7.21166	7.46223	1.03475
393	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Squared	0	9.11845	8.43969	1.08042
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Rooted	1	49.8842	45.2875	1.1015
	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	Measured	1	4490.28	5222.25	1.16301
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Measured	0	2131.42	2218.51	1.04086
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Rooted	0	33.8811	32.7487	1.03458
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Ranked	1	225.719	207.072	1.09005
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Ranked	0	12576	13010	1.03451
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	Squared	1	28895.6	35572.8	1.23108
394	60s ribosomal protein l12. [swissprot;acc:p30050]	Ranked	0	10196.9	9857.79	1.0344
	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). [swissprot;acc:q9y6q5]	Squared	0	70.823	65.5835	1.07989
	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	Measured	1	4490.28	5222.25	1.16301
	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Ranked	1	218.827	238.407	1.08948
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Measured	0	2131.52	2218.58	1.04084
	mad protein (max dimerizer). [swissprot;acc:q05195]	Squared	1	17248.4	21214	1.22991

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/