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 4408 to 4457 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
551 selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Ranked Subtracted 222.156 208.201 13.955
552 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Measured 6503.03 7282.5 779.47
adp-ribosylation factor gtpase activating protein 1 (adp-ribosylation factor 1 gtpase activating protein) (arf1 gap) (arf1-directed gtpase- activating protein) (gap protein). [swissprot;acc:q8n6t3] Squared Divided 27516.2 32720 1.18912
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Rooted Subtracted 63.847 68.8873 5.0403
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Measured Divided 15427.2 13572.8 1.13663
crk-like protein. [swissprot;acc:p46109] Ranked 207.26 194.346 1.06645
dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] Squared Subtracted 22109.6 26989.4 4879.8
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Ranked 222.156 208.201 13.955
nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Rooted Divided 66.082 71.6523 1.08429
553 coatomer beta subunit (beta-coat protein) (beta-cop). [swissprot;acc:p53618] Measured Subtracted 10430.3 9656.4 773.9
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] Squared 14668.3 19547 4878.7
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Rooted 63.847 68.8873 5.0403
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Ranked Divided 207.26 194.346 1.06645
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Subtracted 226.3 212.38 13.92
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Rooted Divided 66.082 71.6523 1.08429
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] Measured 3853.64 4379.71 1.13651
vesicle-associated membrane protein 3 (vamp-3) (synaptobrevin 3) (cellubrevin) (ceb). [swissprot;acc:q15836] Squared 27516.2 32720 1.18912
554 dendritic cell protein. [refseq;acc:nm_006360] Measured Subtracted 6593.17 7364.55 771.38
eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] Rooted 50.1918 55.2294 5.0376
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Divided 66.0829 71.6462 1.08419
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] Squared Subtracted 14690.3 19560.2 4869.9
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] Measured Divided 14830.5 13050.3 1.13641
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Squared 8426.68 10010.8 1.18799
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Ranked 207.26 194.346 1.06645
t54 protein. [swissprot;acc:q92917] Subtracted 226.3 212.38 13.92
555 cbf1 interacting corepressor. [refseq;acc:nm_004882] 227.86 213.945 13.915
importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410] Squared 30826.4 35693.3 4866.9
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Measured 6593.17 7364.55 771.38
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Ranked Divided 207.26 194.346 1.06645
pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328] Rooted Subtracted 68.4526 73.4852 5.0326
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). [swissprot;acc:p34991] Squared Divided 8426.68 10010.8 1.18799
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Measured 6167.93 7007.7 1.13615
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Rooted 59.7823 64.7895 1.08376
556 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Measured Subtracted 6593.17 7364.55 771.38
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Ranked Divided 207.27 194.368 1.06638
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Squared Subtracted 29554.6 34419.4 4864.8
evolutionarily conserved g-patch domain containing. [refseq;acc:nm_018025] Ranked 227.86 213.945 13.915
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. [refseq;acc:nm_018315] Squared Divided 8426.68 10010.8 1.18799
flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Measured 6167.93 7007.7 1.13615
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Rooted Subtracted 68.433 73.4502 5.0172
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Divided 66.0911 71.6061 1.08345
557 cpz gene product. [refseq;acc:nm_003652] Measured Subtracted 6593.17 7364.55 771.38
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Squared Divided 8426.68 10010.8 1.18799
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529] Ranked 207.272 194.371 1.06637
inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Measured 6167.93 7007.7 1.13615
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Rooted Subtracted 55.5489 50.535 5.0139
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Squared 29554.6 34419.4 4864.8
shwachman-bodian-diamond syndrome protein (cgi-97). [swissprot;acc:q9y3a5] Ranked 216.557 230.362 13.805
t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Rooted Divided 97.1967 105.302 1.08339
558 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Measured Subtracted 6593.17 7364.55 771.38

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/