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 1201 to 1250 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
601 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] Subtracted 4533.74 5279.4 745.66
symplekin. [swissprot;acc:q92797] Divided 15213.4 13418.1 1.1338
602 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] 4864.66 5514.87 1.13366
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] Subtracted 4533.74 5279.4 745.66
603 ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Divided 4864.66 5514.87 1.13366
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] Subtracted 4533.74 5279.4 745.66
604 rw1 protein (fragment). [swissprot;acc:q92545]
vinculin (metavinculin). [swissprot;acc:p18206] Divided 5958.23 6743.37 1.13177
605 probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 6143.52 6950.75 1.1314
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Subtracted 6079.26 6824.47 745.21
606 calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Divided 6148.94 6955.76 1.13121
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Subtracted 10231.8 9487.34 744.46
607 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]
likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] Divided 14976.4 13246.6 1.13058
608 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 2234.68 2978.53 743.85
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Divided 4510.61 5098.74 1.13039
609 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 3886.62 3438.82 1.13022
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 2234.73 2978.57 743.84
610 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] 2236.61 2980.35 743.74
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Divided 8430.03 9518.11 1.12907
611 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 5148.71 5811.74 1.12878
fibulin-2 precursor. [swissprot;acc:p98095] Subtracted 8670.59 9412.9 742.31
612 cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] 5480.24 6222.04 741.8
eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Divided 3975.77 4485.05 1.1281
613 transforming protein rhoc (h9). [swissprot;acc:p08134] Subtracted 5480.24 6222.04 741.8
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Divided 3975.77 4485.05 1.1281
614 solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 11222.2 9948.93 1.12798
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Subtracted 5480.24 6222.04 741.8
615 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] Divided 11222.2 9948.93 1.12798
616 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798]
transforming protein rhoa (h12). [swissprot;acc:p06749] Subtracted 5480.24 6222.04 741.8
617 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Divided 5162.52 5822.47 1.12783
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] Subtracted 4532.73 5269.33 736.6
618 dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1] 6327.86 7064.13 736.27
nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [swissprot;acc:q13232] Divided 7878.27 8879.08 1.12703
619 nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 3879.99 4371.24 1.12661
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Subtracted 6811.2 7547.35 736.15
620 aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] 6807.78 7543.28 735.5
ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Divided 6227.87 7012.9 1.12605
621 ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647] 4115.39 4633.96 1.12601
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70] Subtracted 6805.86 7540.99 735.13
622 mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Divided 6228.42 7013.21 1.126
ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977] Subtracted 6805.45 7540.5 735.05
623 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Divided 6228.39 7013.19 1.126
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Subtracted 4490.28 5222.25 731.97
624 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Divided 6228.39 7013.19 1.126
625 disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490]
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] Subtracted 5291.92 6020.19 728.27

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/