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 Value Type Gene Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1327 to 1376 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
332 Squared NUBP1 nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] 14464.3 18142.8 1.25432
Rooted SHROOM3 shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] 60.6732 67.2827 1.10894
333 Measured PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 5039.63 5961.83 1.18299
Ranked NEUROD1 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] 312 284 1.09859
Squared NUBP2 nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] 14464.3 18142.8 1.25432
Rooted GTPBP4 nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] 49.0526 54.3781 1.10857
334 Measured SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] 14924.4 17655.2 1.18298
Ranked NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 312 284 1.09859
Squared CANT1 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 64975.9 81151.2 1.24894
Rooted PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 58.6096 64.9655 1.10844
335 Measured DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 1.18181
Ranked CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 312 284 1.09859
Squared C15orf15 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] 30651.3 38253.3 1.24802
Rooted RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] 50.4705 45.5342 1.10841
336 Measured POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 3751.3 4431.34 1.18128
Ranked CDK2AP1 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] 312 284 1.09859
Squared RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 46785.7 58383.2 1.24789
Rooted RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] 50.3167 45.4063 1.10814
337 Measured no value homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 20446.1 24136.4 1.18049
Ranked 60s ribosomal protein l12. [swissprot;acc:p30050] 243.583 267.527 1.0983
Squared HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 46785.7 58383.2 1.24789
Rooted CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] 77.5801 70.0182 1.108
338 Measured HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 1.18049
Ranked no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 267.528 1.0983
Squared HIVEP1 zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] 46785.7 58383.2 1.24789
Rooted CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 77.58 70.0181 1.108
339 Measured HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 20446.1 24136.4 1.18049
Ranked no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 243.583 267.527 1.0983
Squared HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 46785.7 58383.2 1.24789
Rooted CPB2 plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] 77.5797 70.0179 1.108
340 Measured no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 20446.1 24136.4 1.18049
Ranked MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] 235.383 258.476 1.09811
Squared RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 32117 40054 1.24713
Rooted PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 58.4926 64.8047 1.10791
341 Measured HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 20446.1 24136.4 1.18049
Ranked no value 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
Squared RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 32056.4 39965.8 1.24673
Rooted SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 51.9812 57.5858 1.10782
342 Measured HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 20446.1 24136.4 1.18049
Ranked RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] 243.5 267.21 1.09737
Squared HGS hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 70830.5 56822 1.24653
Rooted EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 49.2715 54.5757 1.10765
343 Measured HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 20446.1 24136.4 1.18049
Ranked PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 241.625 265.136 1.0973
Squared COG7 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] 70830.5 56822 1.24653
Rooted no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 50.3169 45.4333 1.10749
344 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 20446.1 24136.4 1.18049
Ranked 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 241.625 265.136 1.0973
Squared IDH2 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] 37226.9 46400.1 1.24641
Rooted PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 49.4233 54.7327 1.10743

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
- Hugo is the HGNC identifier if it exists
- 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/