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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1330 to 1379 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
333 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
334 ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 64975.9 81151.2 1.24894
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Ranked 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
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 14924.4 17655.2 1.18298
335 40s ribosomal protein s11. [swissprot;acc:p04643] Rooted 50.4705 45.5342 1.10841
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked 312 284 1.09859
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Measured 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
336 60s ribosomal protein l11. [swissprot;acc:p39026] Rooted 50.3167 45.4063 1.10814
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 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
337 60s ribosomal protein l12. [swissprot;acc:p30050] Ranked 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
338 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Ranked 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
mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Rooted 77.58 70.0181 1.108
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 46785.7 58383.2 1.24789
339 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Ranked 243.583 267.527 1.0983
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured 20446.1 24136.4 1.18049
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Squared 46785.7 58383.2 1.24789
plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872] Rooted 77.5797 70.0179 1.108
340 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Measured 20446.1 24136.4 1.18049
myelin gene expression factor 2. [refseq;acc:nm_016132] Ranked 235.383 258.476 1.09811
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Rooted 58.4926 64.8047 1.10791
ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared 32117 40054 1.24713
341 60s ribosomal protein l9. [swissprot;acc:p32969] Ranked 240.243 263.798 1.09805
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured 20446.1 24136.4 1.18049
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Rooted 51.9812 57.5858 1.10782
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared 32056.4 39965.8 1.24673
342 40s ribosomal protein s20. [swissprot;acc:p17075] Ranked 243.5 267.21 1.09737
hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Squared 70830.5 56822 1.24653
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Measured 20446.1 24136.4 1.18049
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Rooted 49.2715 54.5757 1.10765
343 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 50.3169 45.4333 1.10749
conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Squared 70830.5 56822 1.24653
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured 20446.1 24136.4 1.18049
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked 241.625 265.136 1.0973
344 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Measured 20446.1 24136.4 1.18049
isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Squared 37226.9 46400.1 1.24641
suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted 49.4233 54.7327 1.10743
345 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 56.2615 62.2958 1.10725
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 24136.4 1.18049
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Squared 35793 44595.3 1.24592

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/