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 658 to 707 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
329 signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] 0 15977.3 15115.5 1.05701
330 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] 1 312 284 1.09859
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152] 0 12320.2 13018.5 1.05668
331 40s ribosomal protein s3a. [swissprot;acc:p49241] 10405.1 10992.4 1.05644
doc-1 related protein (doc-1r). [swissprot;acc:o75956] 1 312 284 1.09859
332 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] 1 312 284 1.09859
333 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 1 312 284 1.09859
334 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 0 8125.5 7697.5 1.0556
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1 312 284 1.09859
335 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 0 8125.5 7697.5 1.0556
336 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] 1 312 284 1.09859
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 0 8125.5 7697.5 1.0556
337 60s ribosomal protein l12. [swissprot;acc:p30050] 1 243.583 267.527 1.0983
glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1 (ec 2.6.1.16) (hexosephosphate aminotransferase 1) (d-fructose-6- phosphate amidotransferase 1) (gfat 1) (gfat1). [swissprot;acc:q06210] 0 12953.2 12273.2 1.05541
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 1 243.583 267.528 1.0983
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] 0 11149.7 10571.4 1.0547
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 1 243.583 267.527 1.0983
tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888] 0 10344.1 10903.3 1.05406
340 guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] 11372.3 10792.3 1.05374
myelin gene expression factor 2. [refseq;acc:nm_016132] 1 235.383 258.476 1.09811
341 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 0 8702.94 9169.98 1.05366
342 40s ribosomal protein s20. [swissprot;acc:p17075] 1 243.5 267.21 1.09737
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 0 10074 10609 1.05311
343 casein kinase i alpha s-like. [refseq;acc:nm_145203] 8356.31 8788.62 1.05173
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 1 241.625 265.136 1.0973
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 0 10540.6 10027.6 1.05116
345 alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] 11563.7 12151.8 1.05086
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 1 242.14 265.697 1.09729
346 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] 0 9267.81 9736.2 1.05054
347 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 7670 7311 1.0491
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 1 242.14 265.697 1.09729
348 adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 265.696 1.09728
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 0 16321 15577 1.04776
349 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
surfeit locus protein 5. [swissprot;acc:q15528] 1 242.14 265.696 1.09728
350 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 0 16321 15577 1.04776
zinc finger protein 291. [swissprot;acc:q9by12] 1 242.14 265.696 1.09728
351 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 0 16321 15577 1.04776
peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 1 242.14 265.696 1.09728
352 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 0 16321 15577 1.04776
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] 1 242.14 265.696 1.09728
353 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 0 16321 15577 1.04776
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] 1 231.73 211.252 1.09694
354 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 0 16321 15577 1.04776

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/