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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 313 to 362 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
79	protein cgi-126 (protein hspc155). [source:swissprot;acc:q9y3c8]	Measured	3074.57	4567.51	1.48558	
79	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Squared	117850	70566.8	1.67005	
79	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [source:swissprot;acc:q00007]	Rooted	63.7477	48.1588	1.3237	
79	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	Ranked	254.693	202.668	1.2567	
80	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [source:swissprot;acc:p31483]	Measured	4133.47	5945.32	1.43834	
80	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [source:swissprot;acc:q00005]	Rooted	63.7477	48.1594	1.32368	
80	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	Squared	117718	70505.9	1.66962	
80	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	Ranked	254.691	202.668	1.25669	
81	cyclin g2. [source:swissprot;acc:q16589]	Squared	117718	70505.9	1.66962	
81	nucleolysin tiar (tia-1 related protein). [source:swissprot;acc:q01085]	Measured	4136.36	5943.56	1.43691	
81	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [source:swissprot;acc:q9y2t4]	Rooted	63.7475	48.1615	1.32362	
81	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	Ranked	254.614	202.646	1.25645	
82	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [source:swissprot;acc:p18847]	Rooted	60.8022	79.5099	1.30768	
82	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Squared	117718	70505.8	1.66962	
82	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	Ranked	267.636	335.359	1.25304	
82	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [source:swissprot;acc:p13641]	Measured	4172.91	5954.48	1.42694	
83	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	Ranked	88.2482	110.265	1.24949	
83	proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [source:swissprot;acc:p01100]	Measured	4932.27	7033.29	1.42597	
83	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [source:swissprot;acc:q15172]	Squared	117718	70505.9	1.66962	
83	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [source:swissprot;acc:p30154]	Rooted	63.6507	48.7127	1.30666	
84	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Squared	117515	70412.3	1.66896	
84	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	Ranked	88.2482	110.265	1.24949	
84	jun dimerization protein. [source:refseq;acc:nm_130469]	Measured	4932.27	7033.29	1.42597	
84	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	Rooted	46.7419	60.9337	1.30362	
85	autophagy protein 12-like (apg12-like). [source:swissprot;acc:o94817]	Squared	67438.6	40697	1.65709	
85	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [source:swissprot;acc:p23511]	Rooted	46.7419	60.9337	1.30362	
85	fos-related antigen 2. [source:swissprot;acc:p15408]	Measured	4941.95	7037.11	1.42395	
85	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	Ranked	88.2482	110.265	1.24949	
86	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	Ranked	88.2482	110.265	1.24949	
86	protein fosb (g0/g1 switch regulatory protein 3). [source:swissprot;acc:p53539]	Measured	4942.49	7037.32	1.42384	
86	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [source:swissprot;acc:p30153]	Rooted	63.6205	48.8838	1.30146	
86	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [source:swissprot;acc:p01116]	Squared	105500	64146.3	1.64468	
87	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	Rooted	42.2825	54.9687	1.30003	
87	fos-related antigen 1 (fra-1). [source:swissprot;acc:p15407]	Measured	4944.3	7038.04	1.42347	
87	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [source:swissprot;acc:q9uq13]	Squared	105482	64136.9	1.64464	
87	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	Ranked	88.2482	110.265	1.24949	
88	hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	Ranked	88.2482	110.265	1.24949	
88	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	Measured	2411.93	1695.45	1.42259	
88	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [source:swissprot;acc:p49810]	Rooted	37.3005	48.4141	1.29795	
88	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [source:swissprot;acc:o15211]	Squared	105482	64137.2	1.64463	
89	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	Measured	2414.22	1698.12	1.4217	
89	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Ranked	88.2482	110.265	1.24949	
89	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [source:swissprot;acc:p34991]	Rooted	37.3005	48.4141	1.29795	
89	transforming protein p21/h-ras-1 (c-h-ras). [source:swissprot;acc:p01112]	Squared	105473	64132.3	1.64462	
90	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [source:refseq;acc:nm_018315]	Rooted	37.3005	48.4141	1.29795	
90	necdin. [source:swissprot;acc:q99608]	Ranked	88.2482	110.265	1.24949	
90	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	Measured	2414.77	1698.75	1.4215	
90	transforming protein n-ras. [source:swissprot;acc:p01111]	Squared	105469	64130.2	1.64461	
91	cullin homolog 2 (cul-2). [source:swissprot;acc:q13617]	Rooted	37.3005	48.4141	1.29795	
91	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Ranked	88.2482	110.265	1.24949	

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