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 1230 to 1279 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
615 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
626 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Divided 6228.39 7013.19 1.126
regulator of chromosome condensation (cell cycle regulatory protein). [swissprot;acc:p18754] Subtracted 8618.32 9340.98 722.66
627 limkain b1. [refseq;acc:nm_019081] Divided 6228.39 7013.19 1.126
zinc finger homeobox protein 1b (smad interacting protein 1) (smadip1) (hrihfb2411). [swissprot;acc:o60315] Subtracted 8618.32 9340.98 722.66
628 putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Divided 6228.39 7013.19 1.126
transcription factor 8 (nil-2-a zinc finger protein) (negative regulator of il2). [swissprot;acc:p37275] Subtracted 8618.32 9340.98 722.66
629 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Divided 6228.39 7013.19 1.126
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] Subtracted 5201.41 4479.76 721.65
630 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Divided 6228.39 7013.19 1.126
631 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] Subtracted 5201.41 4479.76 721.65
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Divided 6228.39 7013.19 1.126
632 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] Subtracted 5201.41 4479.76 721.65
633 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Divided 6228.39 7013.19 1.126
634 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0]
leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Subtracted 5201.41 4479.76 721.65
635 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Divided 6228.97 7013.53 1.12595
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Subtracted 5201.41 4479.76 721.65
636 proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Divided 5713.41 6432.92 1.12593
thymic stromal co-transporter. [refseq;acc:nm_033051] Subtracted 5201.41 4479.76 721.65
637 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 4889.21 5610.52 721.31
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Divided 7756.51 8731.76 1.12573
638 n-myc proto-oncogene protein. [swissprot;acc:p04198] Subtracted 4889.71 5610.69 720.98
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Divided 7755.69 8730.74 1.12572
639 ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Subtracted 4890.51 5610.95 720.44
nucleoside diphosphate kinase b (ec 2.7.4.6) (ndk b) (ndp kinase b) (nm23-h2) (c-myc purine-binding transcription factor puf). [swissprot;acc:p22392] Divided 7753.59 8728.13 1.12569
640 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] Subtracted 4890.51 5610.95 720.44

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/