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 Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 3130 to 3179 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
392	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
	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	Rooted	1	58.6533	64.5958	1.10132
	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. [refseq;acc:nm_015975]		0	13.4343	13.8963	1.03439
395	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]		0	32.0326	30.9731	1.03421
	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked	1	218.827	238.407	1.08948
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Ranked	0	10195.5	9856.7	1.03437
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Measured	0	2131.83	2218.82	1.04081
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Squared	1	17254.4	21218.1	1.22972
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Rooted	1	50.0423	45.4523	1.10098
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Squared	0	6777.96	6288.98	1.07775
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Measured	1	4532.73	5269.33	1.16251
396	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Ranked	0	10194.8	9856.12	1.03436
	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Rooted	1	116.797	106.111	1.10071
	histone h2b. [refseq;acc:nm_175055]	Measured	0	2131.91	2218.89	1.0408
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Squared	1	17256.5	21219.6	1.22966
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Ranked	1	240.801	262.34	1.08945
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Squared	0	6749.52	6272.46	1.07606
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Measured	1	6563.65	7627.29	1.16205
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	Rooted	0	32.0372	30.9782	1.03419
397	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Ranked		10006.9	9676.53	1.03414
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Squared		80280.6	74715.1	1.07449
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Measured		2131.93	2218.9	1.04079
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Squared	1	17257.5	21220.3	1.22963
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Measured		5367.04	6233.12	1.16137
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Rooted		116.792	106.107	1.1007
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Rooted	0	18.8643	18.2434	1.03403
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	Ranked	1	110.689	101.613	1.08932
398	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Ranked	0	16699.2	17267.9	1.03406
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Measured	0	2132.04	2218.98	1.04078
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Squared	1	18929.1	23222.8	1.22683

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/