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 Network Comparison Type description Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1336 to 1385 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
334 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] Measured 14924.4 17655.2 1.18298
335 C15orf15 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
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Ranked 312 284 1.09859
DDX56 probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Measured 3494.31 4129.6 1.18181
RPS11 40s ribosomal protein s11. [swissprot;acc:p04643] Rooted 50.4705 45.5342 1.10841
336 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] Ranked 312 284 1.09859
POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Measured 3751.3 4431.34 1.18128
RBPJ j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Squared 46785.7 58383.2 1.24789
RPL11 60s ribosomal protein l11. [swissprot;acc:p39026] Rooted 50.3167 45.4063 1.10814
337 no value 60s ribosomal protein l12. [swissprot;acc:p30050] Ranked 243.583 267.527 1.0983
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 20446.1 24136.4 1.18049
CPA6 carboxypeptidase b precursor. [refseq;acc:nm_020361] Rooted 77.5801 70.0182 1.108
HIVEP3 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] Squared 46785.7 58383.2 1.24789
338 no value 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Ranked 243.583 267.528 1.0983
CPA3 mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088] Rooted 77.58 70.0181 1.108
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] Squared 46785.7 58383.2 1.24789
HOXB4 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Measured 20446.1 24136.4 1.18049
339 no value dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Ranked 243.583 267.527 1.0983
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] Rooted 77.5797 70.0179 1.108
HIVEP2 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Squared 46785.7 58383.2 1.24789
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Measured 20446.1 24136.4 1.18049
340 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]
MYEF2 myelin gene expression factor 2. [refseq;acc:nm_016132] Ranked 235.383 258.476 1.09811
PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Rooted 58.4926 64.8047 1.10791
RRM2B ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] Squared 32117 40054 1.24713
341 no value 60s ribosomal protein l9. [swissprot;acc:p32969] Ranked 240.243 263.798 1.09805
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Measured 20446.1 24136.4 1.18049
RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Squared 32056.4 39965.8 1.24673
SSB lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Rooted 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 hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] Squared 70830.5 56822 1.24653
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Measured 20446.1 24136.4 1.18049
RPS20 40s ribosomal protein s20. [swissprot;acc:p17075] Ranked 243.5 267.21 1.09737
343 no value 60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Rooted 50.3169 45.4333 1.10749
COG7 conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] Squared 70830.5 56822 1.24653
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Measured 20446.1 24136.4 1.18049
PRMT3 protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Ranked 241.625 265.136 1.0973
344 no value 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
IDH2 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
PPAN-P2RY11 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] Rooted 49.4233 54.7327 1.10743
345 CMPK ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked 242.14 265.697 1.09729
DHX15 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted 56.2615 62.2958 1.10725
HSD17B14 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured 20446.1 24136.4 1.18049
SH3GL1 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
346 CSE1L importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 34018.3 42373 1.24559
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Rooted 61.4282 68.0107 1.10716
RPS3 40s ribosomal protein s3. [swissprot;acc:p23396] Ranked 241.612 265.119 1.09729
SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 14229.2 16780.7 1.17931
347 AK3 gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Ranked 242.14 265.697 1.09729

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/