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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 644 to 693 of 12912 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence
Filtered

: 1

Rank	Hugo	description	Value Type	red	green	network_comparison
161	SYNCRIP	ns1-associated protein 1. [refseq;acc:nm_006372]	Rooted	52.7642	61.9019	1.17318
162	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Rooted	52.7642	61.9019	1.17318
	HOXC5	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Squared	173408	242989	1.40126
	MAGEB6B	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Measured	23693.7	18263	1.29736
	NOSTRIN	nostrin. [refseq;acc:nm_052946]	Ranked	209.299	249.187	1.19058
163	no value	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared	173408	242989	1.40126
	no value	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Measured	23693.7	18263	1.29736
	EIF4G1	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Rooted	52.7702	61.8915	1.17285
	SNF8	eap30 subunit of ell complex. [refseq;acc:nm_007241]	Ranked	209.299	249.187	1.19058
164	HOXD4	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Squared	173408	242989	1.40126
	MAGEA9	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Measured	23693.7	18263	1.29736
	MXD1	mad protein (max dimerizer). [swissprot;acc:q05195]	Rooted	55.646	65.1534	1.17086
	SLC39A6	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]	Ranked	209.299	249.187	1.19058
165	GAD2	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]	Ranked	209.299	249.187	1.19058
	HOXB5	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Squared	173408	242989	1.40126
	MAGEA8	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Measured	23693.7	18263	1.29736
	MXI1	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Rooted	55.6486	65.1478	1.1707
166	HOXA5	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Squared	173408	242989	1.40126
	MAGEC1	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured	23693.7	18263	1.29736
	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Rooted	55.6495	65.1458	1.17064
	NAPG	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Ranked	209.299	249.187	1.19058
167	no value	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared	173408	242989	1.40126
	GAD1	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Ranked	209.299	249.187	1.19058
	MAGEA4	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured	23693.7	18263	1.29736
	RAB24	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Rooted	55.65	65.1448	1.17062
168	no value	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Ranked	82.5916	98.0548	1.18722
	no value	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Measured	23693.7	18263	1.29736
	HSD17B14	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Squared	173408	242989	1.40126
	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Rooted	56.3709	65.8949	1.16895
169	ATG3	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	Ranked	82.5916	98.0548	1.18722
	COPS3	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Rooted	62.762	53.7761	1.1671
	MAGEA10	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Measured	23693.7	18263	1.29736
	SYMPK	symplekin. [swissprot;acc:q92797]	Squared	124118	88668.8	1.39979
170	B9D1	b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	Rooted	53.4993	45.9227	1.16499
	CTPS2	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	Squared	96730.5	69286.7	1.39609
	MAGEB4	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Measured	23693.7	18263	1.29736
	TIA1	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Ranked	227.199	192.715	1.17894
171	CTPS	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	Squared	96602.7	69211.2	1.39577
	LASS2	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Rooted	61.6639	71.7355	1.16333
	MAGED2	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Measured	23693.7	18263	1.29736
	TIAL1	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Ranked	227.202	192.823	1.17829
172	CSTF2T	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	Squared	121579	87259.3	1.39331
	SF3B1	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Rooted	56.7592	65.9889	1.16261
	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Ranked	174.667	205.556	1.17685
	TRO	trophinin. [swissprot;acc:q12816]	Measured	23693.7	18263	1.29736
173	BCAR3	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Measured	4579.34	5940.64	1.29727
	MRPS17	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	Rooted	145.551	168.796	1.1597
	SEPT4	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	Squared	82624.3	115061	1.39258
	SNRPD1	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Ranked	227.032	193.056	1.17599
174	DGCR14	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	Ranked	335	286	1.17133

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
- 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/