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

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Showing element 1508 to 1557 of 16578 in total

Value Type	Ranked
Filtered	1

Rank	Hugo	Network Comparison Type	description	Interaction Map	red	green	network_comparison	
377	POLR1A	Divided	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	High confidence	242.691	265.481	1.09391	
378	FEM1B	Subtracted	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [source:refseq;acc:nm_015322]	High confidence	248.152	267.226	19.074	
378	LDHC	Divided	l-lactate dehydrogenase c chain (ec 1.1.1.27) (ldh-c) (ldh testis subunit) (ldh-x). [source:swissprot;acc:p07864]	Low confidence	205.928	198.554	1.03714	
378	RPL30	Divided	60s ribosomal protein l30. [source:swissprot;acc:p04645]	High confidence	242.593	265.365	1.09387	
378	SLC35E1	Subtracted	solute carrier family 35, member e1. [source:refseq;acc:nm_024881]	Low confidence	203.661	211.03	7.369	
379	AK2	Divided	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	High confidence	241.509	264.163	1.0938	
379	LDHA	Divided	l-lactate dehydrogenase a chain (ec 1.1.1.27) (ldh-a) (ldh muscle subunit) (ldh-m). [source:swissprot;acc:p00338]	Low confidence	205.928	198.554	1.03714	
379	LRRC3	Subtracted	leucine-rich repeat protein lrrc3 precursor. [source:swissprot;acc:q9by71]	High confidence	248.152	267.226	19.074	
379	MXD4	Subtracted	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Low confidence	205.921	198.554	7.367	
380		Divided	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	High confidence	242.109	264.79	1.09368	
380	LAMC1	Subtracted	laminin gamma-1 chain precursor (laminin b2 chain). [source:swissprot;acc:p11047]	High confidence	248.152	267.226	19.074	
380	LDHB	Divided	l-lactate dehydrogenase b chain (ec 1.1.1.27) (ldh-b) (ldh heart subunit) (ldh-h). [source:swissprot;acc:p07195]	Low confidence	205.928	198.554	1.03714	
380	RAB24	Subtracted	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Low confidence	205.918	198.554	7.364	
381	CLASP1	Divided	clip-associating protein 1; drosophila 'multiple asters' (mast)-like homolog 1. [source:refseq;acc:nm_015282]	Low confidence	205.928	198.554	1.03714	
381	POLE4	Subtracted	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Low confidence	205.821	198.494	7.327	
381	SLC46A2	Subtracted	thymic stromal co-transporter. [source:refseq;acc:nm_033051]	High confidence	248.152	267.226	19.074	
381	TAF7	Divided	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	High confidence	200.586	183.423	1.09357	
382		Subtracted	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Low confidence	162.755	155.476	7.279	
382	DDX54	Subtracted	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	High confidence	253.852	234.808	19.044	
382	MXI1	Divided	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Low confidence	205.926	198.554	1.03713	
382	TAF7L	Divided	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	High confidence	200.791	183.66	1.09328	
383	HOXB4	Subtracted	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Low confidence	162.755	155.476	7.279	
383	MXD4	Divided	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Low confidence	205.921	198.554	1.0371	
383	RBM39	Divided	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	High confidence	237.862	217.739	1.09242	
383	TRUB1	Subtracted	trub pseudouridine (psi) synthase homolog 1. [source:refseq;acc:nm_139169]	High confidence	236.245	255.113	18.868	
384		Subtracted	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	High confidence	227.575	208.756	18.819	
384	E2F1	Divided	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	High confidence	266.421	244.236	1.09083	
384	HOXC5	Subtracted	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Low confidence	162.755	155.476	7.279	
384	RAB24	Divided	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	Low confidence	205.918	198.554	1.03709	
385		Subtracted	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Low confidence	162.755	155.476	7.279	
385	E2F2	Divided	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	High confidence	266.421	244.236	1.09083	
385	SNRPD3	Divided	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [source:swissprot;acc:p43331]	Low confidence	201.176	193.984	1.03708	
385	SNRPF	Subtracted	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	High confidence	227.575	208.756	18.819	
386	HOXD4	Subtracted	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Low confidence	162.755	155.476	7.279	
386	POLE4	Divided	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Low confidence	205.821	198.494	1.03691	
386	RPS14	Divided	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	High confidence	242.238	264.11	1.09029	
386	RPS9	Subtracted	40s ribosomal protein s9. [source:swissprot;acc:p46781]	High confidence	238.986	257.784	18.798	
387		Divided	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	High confidence	242.238	264.11	1.09029	
387	ATG4A	Subtracted	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	High confidence	56.6768	75.3531	18.6763	
387	HOXB5	Subtracted	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Low confidence	162.755	155.476	7.279	
387	HTRA1	Divided	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Low confidence	200.057	192.938	1.0369	
388		Divided	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	High confidence	227.575	208.756	1.09015	
388	HOXA5	Subtracted	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Low confidence	162.755	155.476	7.279	
388	HTRA3	Divided	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	Low confidence	200.049	192.942	1.03683	
388	MAP1LC3B	Subtracted	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [source:swissprot;acc:q9gzq8]	High confidence	56.7244	75.3948	18.6704	
389		Subtracted	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Low confidence	162.755	155.476	7.279	
389	HTRA4	Divided	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Low confidence	200.049	192.942	1.03683	
389	MAP1LC3A	Subtracted	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [source:swissprot;acc:q9h492]	High confidence	56.7252	75.3954	18.6702	
389	SNRPF	Divided	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	High confidence	227.575	208.756	1.09015	
390		Divided	solute carrier family 35, member e2. [source:refseq;acc:nm_182838]	Low confidence	203.647	211.144	1.03681	

Legend:
- Rank is the rank after comparing the two networks
- 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/