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 5908 to 5957 of 19268 in total

Value Type

: Ranked

Rank	description	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison
818	gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]	Subtracted	Low confidence	1	204.064	198.895	5.169
	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	Divided	Low confidence	0	10591.4	10615	1.00223
	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]		High confidence	1	168.592	161.452	1.04422
	serine hydrolase-like protein (ec 3.1.-.-). [swissprot;acc:q9h4i8]		Low confidence	1	208.488	203.181	1.02612
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Subtracted	Low confidence	0	12057.9	12035.6	22.3
819	60s ribosomal protein l18a. [swissprot;acc:q02543]	Subtracted	High confidence	1	234.025	224.958	9.067
	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Divided	Low confidence		208.488	203.181	1.02612
	dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954]	Divided	High confidence		228.563	238.668	1.04421
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Subtracted	Low confidence		149.423	144.256	5.167
	lactotransferrin precursor (lactoferrin) [contains: lactoferroxin a; lactoferroxin b; lactoferroxin c]. [swissprot;acc:p02788]	Subtracted		0	13838	13860.3	22.3
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Divided		0	11234.3	11256.8	1.002
820	40s ribosomal protein s19. [swissprot;acc:p39019]	Subtracted	High confidence	1	234.025	224.958	9.067
	actin binding lim protein 2. [refseq;acc:nm_032432]	Divided	Low confidence	1	208.488	203.181	1.02612
	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	Subtracted		0	1543	1521	22
	forkhead box protein o1a (forkhead in rhabdomyosarcoma). [swissprot;acc:q12778]	Subtracted		1	204.497	199.336	5.161
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Divided		0	11097.9	11119.5	1.00195
	mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399]	Divided	High confidence	1	221.716	231.501	1.04413
821	60s ribosomal protein l31. [swissprot;acc:p12947]	Subtracted	High confidence	1	234.025	224.958	9.067
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Divided	Low confidence	0	11173.7	11194.8	1.00189
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]	Subtracted		0	11097.9	11119.5	21.6
	peroxisomal targeting signal 1 receptor (peroxismore receptor 1) (peroxisomal c-terminal targeting signal import receptor) (pts1-bp) (peroxin-5) (pts1 receptor). [swissprot;acc:p50542]	Divided		1	208.488	203.181	1.02612
	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	Divided	High confidence		221.676	231.453	1.0441
	vigilin (high density lipoprotein-binding protein) (hdl-binding protein). [swissprot;acc:q00341]	Subtracted	Low confidence		201.169	196.014	5.155
822	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	Subtracted		0	11832.8	11854.2	21.4
	actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	Divided		1	208.488	203.181	1.02612
	eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884]	Divided	High confidence		243.067	232.805	1.04408
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Subtracted	High confidence		55	46	9
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Divided	Low confidence	0	11173.7	11194.8	1.00189
	regulator of nonsense transcripts 1 (nonsense mrna reducing factor 1) (norf1) (up-frameshift suppressor 1 homolog). [swissprot;acc:q92900]	Subtracted		1	202.069	196.914	5.155
823	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]			0	11173.7	11194.8	21.1
	eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371]			1	205.551	200.398	5.153
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]		High confidence		55	46	9
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Divided	Low confidence		186.275	181.537	1.0261
	transcription factor iib. [refseq;acc:nm_013242]		High confidence		206.068	197.471	1.04354
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]		Low confidence	0	11173.7	11194.8	1.00189
824	myofibrillogenesis regulator 1; trans-activated by hepatitis c virus core protein 2; likely ortholog of mouse brain protein 17. [refseq;acc:nm_022572]	Subtracted	Low confidence	1	200.782	195.631	5.151
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]		High confidence	1	55	46	9
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]		Low confidence	0	11173.7	11194.8	21.1
	olf-1/ebf associated zinc finger protein; smad- and olf-interacting zinc finger protein. [refseq;acc:nm_015069]	Divided	Low confidence	1	204.922	199.711	1.02609
	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]		High confidence	1	206.068	197.471	1.04354
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]		Low confidence	0	12057.9	12035.6	1.00185
825	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]		Low confidence	0	11832.8	11854.2	1.00181
	40s ribosomal protein s3a. [swissprot;acc:p49241]	Subtracted	High confidence	1	225.689	234.674	8.985
	early hematopoietic zinc finger. [refseq;acc:nm_015461]	Divided	Low confidence	1	204.914	199.706	1.02608
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	Subtracted		0	11173.7	11194.8	21.1
	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	Subtracted		1	202.15	197.002	5.148
	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	Divided	High confidence		206.214	197.614	1.04352
826	60 kda tat interactive protein (tip60) (hiv-1 tat interactive protein) (cpla(2) interacting protein). [swissprot;acc:q92993]		High confidence		223.186	213.912	1.04335
	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]		Low confidence		201.026	195.916	1.02608
	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]	Subtracted	Low confidence		192.552	187.412	5.14

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/