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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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1344 to 1393 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
336 Rooted 60s ribosomal protein l11. [swissprot;acc:p39026] 50.3167 45.4063 1.10814
337 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
Squared human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503] 46785.7 58383.2 1.24789
Rooted carboxypeptidase b precursor. [refseq;acc:nm_020361] 77.5801 70.0182 1.108
338 Measured homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 20446.1 24136.4 1.18049
Ranked 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] 243.583 267.528 1.0983
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
Rooted 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 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 20446.1 24136.4 1.18049
Ranked dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] 243.583 267.527 1.0983
Squared human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] 46785.7 58383.2 1.24789
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
340 Measured homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 20446.1 24136.4 1.18049
Ranked myelin gene expression factor 2. [refseq;acc:nm_016132] 235.383 258.476 1.09811
Squared ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713] 32117 40054 1.24713
Rooted nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] 58.4926 64.8047 1.10791
341 Measured homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 20446.1 24136.4 1.18049
Ranked 60s ribosomal protein l9. [swissprot;acc:p32969] 240.243 263.798 1.09805
Squared ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 32056.4 39965.8 1.24673
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 Measured homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 20446.1 24136.4 1.18049
Ranked 40s ribosomal protein s20. [swissprot;acc:p17075] 243.5 267.21 1.09737
Squared hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712] 70830.5 56822 1.24653
Rooted probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 49.2715 54.5757 1.10765
343 Measured homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 20446.1 24136.4 1.18049
Ranked protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] 241.625 265.136 1.0973
Squared conserved oligomeric golgi complex component 7. [swissprot;acc:p83436] 70830.5 56822 1.24653
Rooted 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 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 suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55] 49.4233 54.7327 1.10743
345 Measured retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] 20446.1 24136.4 1.18049
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
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
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
346 Measured septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] 14229.2 16780.7 1.17931
Ranked 40s ribosomal protein s3. [swissprot;acc:p23396] 241.612 265.119 1.09729
Squared importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] 34018.3 42373 1.24559
Rooted grb2-related adaptor protein. [swissprot;acc:q13588] 61.4282 68.0107 1.10716
347 Measured enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 4991.02 5885.09 1.17914
Ranked gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 242.14 265.697 1.09729
Squared small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 16573.6 20637.8 1.24522
Rooted cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 66.4284 60.0004 1.10713
348 Measured splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] 4991.02 5885.09 1.17914
Ranked adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 242.14 265.696 1.09728
Squared golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 42566.2 52985.3 1.24477
Rooted ad24 protein. [refseq;acc:nm_022451] 49.2558 54.5235 1.10695
349 Measured putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 4714.85 5554.38 1.17806

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/