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 2110 to 2159 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
264	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Measured	0	3336.48	2957.12	1.12829
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Rooted	0	11.0015	9.99917	1.10024
	wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768]		1	66.1122	74.1438	1.12148
265	40s ribosomal protein s29. [swissprot;acc:p30054]		0	26.1023	28.6733	1.0985
	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Squared		3687.69	4640.77	1.25845
	60s ribosomal protein l9. [swissprot;acc:p32969]	Measured		1685.44	1894.01	1.12375
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Ranked		13653.8	14874	1.08937
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Squared	1	26157.6	20236.2	1.29261
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Ranked		225.217	202.459	1.11241
	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Rooted		56.031	62.8281	1.12131
	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Measured		24806.9	20369.9	1.21782
266	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]		0	1475.05	1312.91	1.1235
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]		1	24806.9	20369.9	1.21782
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Squared	0	3687.33	4640.32	1.25845
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Squared	1	26157.6	20236.2	1.29261
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]	Rooted	1	66.1064	74.1074	1.12103
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Ranked	0	13483.3	14685.4	1.08915
	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	Rooted	0	39.5626	36.099	1.09595
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Ranked	1	241.07	267.88	1.11121
267	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	Ranked		241.07	267.88	1.11121
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Squared		26157.6	20236.2	1.29261
	mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683]	Squared	0	181.291	144.478	1.2548
	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	Measured	1	14021.4	11523	1.21682
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	Rooted	0	12.9585	14.1963	1.09552
	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Ranked	0	8054.34	8772.02	1.0891
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	Rooted	1	66.1064	74.1073	1.12103
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Measured	0	1475.05	1312.91	1.1235
268	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	Measured	1	24473.9	20127.8	1.21593
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Ranked	1	271.016	244.167	1.10996
	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	Measured	0	604.529	538.094	1.12346
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	Squared	1	26157.6	20236.2	1.29261
	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Ranked	0	14257.4	13134.5	1.08549
	protein cgi-147. [swissprot;acc:q9y3e5]	Squared	0	75129.2	94178	1.25355
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Rooted	1	66.1064	74.1074	1.12103
	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	Rooted	0	13.0249	14.2577	1.09465
269	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	Measured		1217.92	1367.83	1.12309
	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Squared		4121.56	5159.2	1.25176
	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	Ranked	1	241.373	267.352	1.10763
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Ranked	0	12463.5	11482.6	1.08542
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Rooted	0	90.4079	98.9265	1.09422
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Squared	1	26157.6	20236.2	1.29261
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]	Rooted		66.1064	74.1074	1.12103
	u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777]	Measured		4590.18	5575.52	1.21466
270	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Squared	0	2569.37	3201.81	1.24615
	crk-like protein. [swissprot;acc:p46109]	Rooted	1	66.1064	74.1074	1.12103
	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	Ranked	0	10735.1	9891.37	1.0853
	fad synthetase. [refseq;acc:nm_025207]	Ranked	1	241.373	267.352	1.10763
	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	Measured	1	23640.2	19479.8	1.21358
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	Measured	0	1217.96	1367.88	1.12309
	transcription factor iib. [refseq;acc:nm_013242]	Squared	1	64739.9	50300.6	1.28706

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/