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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1333 to 1382 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
334 CANT1 Squared ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793] 64975.9 81151.2 1.24894
NEUROD4 Ranked neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 312 284 1.09859
PLRG1 Rooted pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 58.6096 64.9655 1.10844
SEPT4 Measured 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
335 C15orf15 Squared 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
CHD5 Ranked chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 312 284 1.09859
DDX56 Measured probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] 3494.31 4129.6 1.18181
RPS11 Rooted 40s ribosomal protein s11. [swissprot;acc:p04643] 50.4705 45.5342 1.10841
336 CDK2AP1 Ranked 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
POLE4 Measured dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 3751.3 4431.34 1.18128
RBPJ Squared j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] 46785.7 58383.2 1.24789
RPL11 Rooted 60s ribosomal protein l11. [swissprot;acc:p39026] 50.3167 45.4063 1.10814
337 no value Measured 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
CPA6 Rooted carboxypeptidase b precursor. [refseq;acc:nm_020361] 77.5801 70.0182 1.108
HIVEP3 Squared human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 46785.7 58383.2 1.24789
338 no value Ranked 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 267.528 1.0983
CPA3 Rooted mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] 77.58 70.0181 1.108
HIVEP1 Squared 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
HOXB4 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 1.18049
339 no value Ranked dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 243.583 267.527 1.0983
CPB2 Rooted 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
HIVEP2 Squared human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 46785.7 58383.2 1.24789
HOXC5 Measured homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 20446.1 24136.4 1.18049
340 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
MYEF2 Ranked myelin gene expression factor 2. [refseq;acc:nm_016132] 235.383 258.476 1.09811
PRPF19 Rooted nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 58.4926 64.8047 1.10791
RRM2B Squared ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 32117 40054 1.24713
341 no value Ranked 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
HOXD4 Measured homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 20446.1 24136.4 1.18049
RRM1 Squared ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 32056.4 39965.8 1.24673
SSB Rooted lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] 51.9812 57.5858 1.10782
342 EBNA1BP2 probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 49.2715 54.5757 1.10765
HGS Squared hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 70830.5 56822 1.24653
HOXB5 Measured homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 20446.1 24136.4 1.18049
RPS20 Ranked 40s ribosomal protein s20. [swissprot;acc:p17075] 243.5 267.21 1.09737
343 no value Rooted 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] 50.3169 45.4333 1.10749
COG7 Squared conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] 70830.5 56822 1.24653
HOXA5 Measured homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 20446.1 24136.4 1.18049
PRMT3 Ranked protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 241.625 265.136 1.0973
344 no value 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
IDH2 Squared 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
PPAN-P2RY11 Rooted suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 49.4233 54.7327 1.10743
345 CMPK Ranked ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 242.14 265.697 1.09729
DHX15 Rooted 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
HSD17B14 Measured retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 20446.1 24136.4 1.18049
SH3GL1 Squared 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] 35793 44595.3 1.24592
346 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 34018.3 42373 1.24559
GRAP Rooted grb2-related adaptor protein. [swissprot;acc:q13588] 61.4282 68.0107 1.10716

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/