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 2658 to 2707 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
333 deltex 2. [refseq;acc:nm_020892] Measured Subtracted 1618.84 2651.88 1033.04
myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Squared 19321 12542.6 6778.4
neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Ranked Divided 312 284 1.09859
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Measured 5039.63 5961.83 1.18299
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4] Rooted 49.0526 54.3781 1.10857
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Squared 14464.3 18142.8 1.25432
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Ranked Subtracted 265.634 244.304 21.33
334 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] Squared Divided 64975.9 81151.2 1.24894
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured Subtracted 1629.21 2662.12 1032.91
e-1 enzyme. [refseq;acc:nm_021204] Squared 30903.8 37638.1 6734.3
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Ranked Divided 312 284 1.09859
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Rooted 58.6096 64.9655 1.10844
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Ranked Subtracted 232.473 211.207 21.266
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] Measured Divided 14924.4 17655.2 1.18298
tuftelin-interacting protein 11 (hspc006). [swissprot;acc:q9ubb9] Rooted Subtracted 58.2964 65.5926 7.2962
335 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 50.4705 45.5342 1.10841
60s ribosomal protein l24 (l30). [swissprot;acc:p38663] Squared Subtracted 30924.3 37652.3 6728
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked Divided 312 284 1.09859
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Rooted Subtracted 52.7146 60.0088 7.2942
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Ranked 223.273 202.423 20.85
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Measured Divided 3494.31 4129.6 1.18181
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Squared 30651.3 38253.3 1.24802
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Measured Subtracted 1631.67 2664.55 1032.88
336 60s ribosomal protein l11. [swissprot;acc:p39026] Rooted Divided 50.3167 45.4063 1.10814
acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510] Squared Subtracted 36109.8 42811.6 6701.8
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] Ranked Divided 312 284 1.09859
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Measured 3751.3 4431.34 1.18128
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 46785.7 58383.2 1.24789
kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Measured Subtracted 1631.67 2664.55 1032.88
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Rooted 59.4073 66.7002 7.2929
rna polymerase i associated factor 53. [refseq;acc:nm_022490] Ranked 241.045 261.874 20.829
337 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 243.583 267.527 1.0983
carboxypeptidase b precursor. [refseq;acc:nm_020361] Rooted 77.5801 70.0182 1.108
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 20446.1 24136.4 1.18049
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Squared 46785.7 58383.2 1.24789
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] Measured Subtracted 1631.67 2664.55 1032.88
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Squared 28895.6 35572.8 6677.2
paxillin. [swissprot;acc:p49023] Rooted 59.4073 66.7002 7.2929
source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] Ranked 200.691 179.88 20.811
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 243.583 267.528 1.0983
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 20446.1 24136.4 1.18049
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Squared Subtracted 28895.6 35572.8 6677.2
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Measured 1631.67 2664.55 1032.88
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Rooted Divided 77.58 70.0181 1.108
metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted 52.7557 60.035 7.2793
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] Ranked 200.691 179.88 20.811
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] Squared Divided 46785.7 58383.2 1.24789
339 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Rooted Subtracted 52.7936 60.0592 7.2656
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Ranked Divided 243.583 267.527 1.0983
dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] Subtracted 200.691 179.88 20.811

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/