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

Results: HTML CSV LaTeX

Showing element 744 to 793 of 66312 in total

Filtered

: 1

Rank	Hugo	description	Network Comparison Type	Value Type	Interaction Map	red	network_comparison	green
47	MAGEA8	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Subtracted	Squared	Low confidence	82347.8	20466.3	61881.5
	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]	Divided	Squared	Low confidence	82347.8	1.33073	61881.5
	MAGEE2	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	Rooted	High confidence	137.446	16.623	120.823
	NFE2L2	nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236]	Divided	Measured	Low confidence	8313.02	1.16027	9645.34
	RAB11FIP4	rab11-family interacting protein 4. [refseq;acc:nm_032932]	Subtracted	Measured		7407.56	1289.14	8696.7
	RAB11FIP4	rab11-family interacting protein 4. [refseq;acc:nm_032932]		Rooted		73.6221	7.8723	81.4944
	TEX28P2	testis-specific protein tex28. [swissprot;acc:o15482]		Ranked		259.517	24.5	235.017
	TMEM132A	gbp protein isoform a. [refseq;acc:nm_017870]	Divided		High confidence	325.586	1.26938	256.492
	TOB2	tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106]	Subtracted			350	60	290
48	no value	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Subtracted	Rooted		137.446	16.623	120.823
	no value	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Divided	Ranked	Low confidence	242.742	1.11751	217.217
	BACH2	transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9]		Measured	Low confidence	8313.02	1.16027	9645.34
	CDK2AP2	doc-1 related protein (doc-1r). [swissprot;acc:o75956]		Measured	High confidence	779.167	1.78438	1390.33
	FOSB	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]		Rooted	Low confidence	66.6504	1.13097	75.3798
	GABARAP	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		Ranked	High confidence	65.4586	1.26868	83.0461
	GOSR2	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]	Subtracted	Ranked	Low confidence	259.517	24.5	235.017
	LASS2	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Divided	Squared	High confidence	6300.2	1.69891	10703.5
	MAGEC1	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Subtracted		Low confidence	82347.8	20466.3	61881.5
	PAPOLG	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	Subtracted		High confidence	210199	73561	136638
	PBK	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492]	Divided	Rooted	High confidence	27.7254	1.58807	44.0299
	RAB11FIP3	eferin. [swissprot;acc:o75154]	Subtracted	Measured	Low confidence	7407.56	1289.14	8696.7
	RAB11FIP3	eferin. [swissprot;acc:o75154]		Rooted	Low confidence	73.6221	7.8723	81.4944
	TOB1	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]		Ranked	High confidence	350	60	290
	TRO	trophinin. [swissprot;acc:q12816]	Divided	Squared	Low confidence	82347.8	1.33073	61881.5
	WDR33	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Subtracted	Measured	High confidence	24806.9	4437	20369.9
49	no value	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Divided	Squared	Low confidence	122475	1.30449	159767
	ARRB2	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	Ranked	High confidence	133	1.26667	105
	CPEB3	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Subtracted	Rooted	Low confidence	48.8531	7.854	56.7071
	CPSF1	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]		Measured	High confidence	24806.9	4437	20369.9
	CSTF3	cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]		Squared		201896	69990	131906
	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]		Ranked		350	60	290
	FOSL1	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]	Divided	Rooted	Low confidence	66.6623	1.1307	75.3751
	KHDRBS3	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558]	Divided		High confidence	27.7254	1.58807	44.0299
	MAGEA11	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Subtracted		High confidence	137.446	16.623	120.823
	MAGEA4	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Subtracted	Squared	Low confidence	82347.8	20466.3	61881.5
	MAP1LC3B	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Divided	Measured	Low confidence	13470.1	1.1558	11654.4
	NEUROD6	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	Divided		High confidence	779.167	1.78438	1390.33
	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]	Subtracted		Low confidence	11141.5	1209.6	12351.1
	STAMBPL1	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Divided	Squared	High confidence	28994.2	1.69212	17134.8
	TBX19	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Divided	Ranked	Low confidence	225.438	1.11289	202.569
	TBX19		Subtracted	Ranked	Low confidence	225.438	22.869	202.569
50	no value	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]		Squared	High confidence	173408	69581	242989
	no value	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]		Squared	Low confidence	82347.8	20466.3	61881.5
	ARRB1	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Divided	Ranked	High confidence	133	1.26667	105
	CHMP2A	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]		Squared	High confidence	28994.2	1.69212	17134.8
	CPD	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976]		Rooted	Low confidence	202.235	1.13003	178.965
	CPEB4	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]	Subtracted	Ranked	High confidence	350	60	290
	CPEB4			Rooted	Low confidence	48.8781	7.8472	56.7253
	CPSF2	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]		Measured	High confidence	24473.9	4346.1	20127.8
	HOXB4	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Divided	Squared	Low confidence	122475	1.30449	159767

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/