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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1551 to 1600 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Value Type	description	red	green	network_comparison	
388	Squared	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [source:sptrembl;acc:q9nq03]	40315.7	49716.4	1.23318	
388	Rooted	serine racemase (ec 5.1.1.-). [source:swissprot;acc:q9gzt4]	50.3345	45.6718	1.10209	
389	Measured	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [source:swissprot;acc:p26196]	4533.74	5279.4	1.16447	
389	Ranked	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	227.575	208.756	1.09015	
389	Squared	arginyl-trna synthetase-like; arginine-trna ligase. [source:refseq;acc:nm_020320]	31819.7	39222.2	1.23264	
389	Rooted	60s ribosomal protein l34. [source:swissprot;acc:p49207]	50.3345	45.6718	1.10209	
390	Measured	rw1 protein (fragment). [source:swissprot;acc:q92545]	4533.74	5279.4	1.16447	
390	Ranked	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	241.828	263.62	1.09011	
390	Squared	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	28895.6	35572.8	1.23108	
390	Rooted	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [source:swissprot;acc:q9y2r3]	50.3345	45.6718	1.10209	
391	Measured	tar dna-binding protein-43 (tdp-43). [source:swissprot;acc:q13148]	3658.76	3144.39	1.16358	
391	Ranked	40s ribosomal protein s16. [source:swissprot;acc:p17008]	241.828	263.62	1.09011	
391	Squared	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [source:swissprot;acc:q14974]	28895.6	35572.8	1.23108	
391	Rooted	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [source:swissprot;acc:p38378]	50.3345	45.6718	1.10209	
392	Measured	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [source:refseq;acc:nm_024072]	3641.89	4236.95	1.16339	
392	Ranked	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	241.83	263.615	1.09008	
392	Squared	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [source:swissprot;acc:o60907]	28895.6	35572.8	1.23108	
392	Rooted	60s ribosomal protein l3-like. [source:swissprot;acc:q92901]	50.3313	45.6913	1.10155	
393	Measured	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [source:swissprot;acc:p06730]	4490.28	5222.25	1.16301	
393	Ranked	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	225.719	207.072	1.09005	
393	Squared	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [source:swissprot;acc:q9bq87]	28895.6	35572.8	1.23108	
393	Rooted	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [source:swissprot;acc:p24928]	49.8842	45.2875	1.1015	
394	Measured	bai1-associated protein 3; bai-associated protein 3. [source:refseq;acc:nm_003933]	4490.28	5222.25	1.16301	
394	Ranked	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	218.827	238.407	1.08948	
394	Squared	mad protein (max dimerizer). [source:swissprot;acc:q05195]	17248.4	21214	1.22991	
394	Rooted	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [source:swissprot;acc:o60508]	58.6533	64.5958	1.10132	
395	Measured	splicing factor 4 isoform b; rna-binding protein. [source:refseq;acc:nm_021164]	4532.73	5269.33	1.16251	
395	Ranked	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	218.827	238.407	1.08948	
395	Squared	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	17254.4	21218.1	1.22972	
395	Rooted	protein translation factor sui1 homolog (sui1iso1). [source:swissprot;acc:p41567]	50.0423	45.4523	1.10098	
396	Measured	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	6563.65	7627.29	1.16205	
396	Ranked	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	240.801	262.34	1.08945	
396	Squared	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	17256.5	21219.6	1.22966	
396	Rooted	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	116.797	106.111	1.10071	
397	Measured	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	5367.04	6233.12	1.16137	
397	Ranked	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	110.689	101.613	1.08932	
397	Squared	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [source:refseq;acc:nm_031300]	17257.5	21220.3	1.22963	
397	Rooted	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	116.792	106.107	1.1007	
398	Measured	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	5084.26	5904.1	1.16125	
398	Ranked	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	218.818	238.358	1.0893	
398	Squared	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [source:refseq;acc:nm_032549]	18929.1	23222.8	1.22683	
398	Rooted	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]	116.707	106.044	1.10055	
399	Measured	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [source:swissprot;acc:p36544]	5201.41	4479.76	1.16109	
399	Ranked	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	207.889	226.226	1.08821	
399	Squared	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [source:swissprot;acc:p21378]	18929.1	23222.8	1.22683	
399	Rooted	cyclin g2. [source:swissprot;acc:q16589]	116.707	106.044	1.10055	
400	Measured	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [source:swissprot;acc:o43306]	5201.41	4479.76	1.16109	
400	Ranked	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	207.908	226.218	1.08807	
400	Squared	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	39478.8	48419	1.22646	
400	Rooted	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	116.707	106.044	1.10055	

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/