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.


Navigation/Query Panel:
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 2780 to 2829 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
695 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] Measured 7725.1 8647.74 1.11943
696 4-aminobutyrate aminotransferase, mitochondrial precursor (ec 2.6.1.19) (gamma-amino-n-butyrate transaminase) (gaba transaminase) (gaba aminotransferase) (gaba-at) (gaba-t). [swissprot;acc:p80404] Squared 22778.5 26693.1 1.17186
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629] Measured 7725.1 8647.74 1.11943
pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322] Rooted 68.433 73.4502 1.07332
sr rich protein. [refseq;acc:nm_032870] Ranked 225.293 213.64 1.05455
697 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] 220.444 209.113 1.05419
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Squared 22778.5 26693.1 1.17186
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] Rooted 63.1944 67.8162 1.07314
sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962] Measured 7105.27 7953.71 1.11941
698 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] 7101.95 7949.85 1.11939
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Rooted 128.909 120.173 1.0727
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Ranked 220.437 209.118 1.05413
red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666] Squared 17850.2 20913.9 1.17163
699 ataxin 2 related protein isoform a; ataxin-2 domain protein. [refseq;acc:nm_007245] Rooted 57.0263 61.1552 1.0724
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Ranked 220.438 209.118 1.05413
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Measured 7101.94 7949.84 1.11939
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Squared 18148.6 21253.1 1.17106
700 40s ribosomal protein s28. [swissprot;acc:p25112] Measured 7161.14 8015.92 1.11936
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Rooted 57.0263 61.1552 1.0724
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Ranked 220.438 209.118 1.05413
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Squared 19072.5 22327.5 1.17066
701 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] 25852.2 30258.6 1.17045
disks large-associated protein 1 (dap-1) (guanylate kinase-associated protein) (hgkap) (sap90/psd-95-associated protein 1) (sapap1) (psd- 95/sap90 binding protein 1). [swissprot;acc:o14490] Ranked 220.438 209.118 1.05413
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Measured 7802.31 8731.82 1.11913
ras-related protein rab-37. [swissprot;acc:q96ax2] Rooted 51.4945 48.0189 1.07238
702 putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Ranked 220.438 209.118 1.05413
ras-related protein rab-26. [swissprot;acc:q9ulw5] Rooted 51.4945 48.0189 1.07238
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Measured 7067.46 7909.27 1.11911
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Squared 25114 29386 1.1701
703 dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Rooted 51.4945 48.0189 1.07238
limkain b1. [refseq;acc:nm_019081] Ranked 220.438 209.118 1.05413
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Measured 6912.56 7735.12 1.11899
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Squared 25114 29386 1.1701
704 alpha-nac protein. [sptrembl;acc:q9h009] Measured 6912.27 7734.68 1.11898
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Squared 25114 29386 1.1701
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Ranked 220.438 209.118 1.05413
syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 57.2102 53.3508 1.07234
705 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Ranked 220.438 209.118 1.05413
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Squared 25114 29386 1.1701
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Measured 6912.09 7734.41 1.11897
syntaxin 6. [swissprot;acc:o43752] Rooted 57.2202 53.3639 1.07226
706 cellular modulator of immune recognition. [refseq;acc:nm_145021] Squared 25114 29386 1.1701
di-ras2. [refseq;acc:nm_017594] Measured 6912.08 7734.39 1.11897
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Ranked 220.438 209.118 1.05413
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Rooted 60.6572 64.9858 1.07136
707 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Measured 5317.78 5944.25 1.11781
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Ranked 220.438 209.118 1.05413
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Rooted 74.8348 80.1352 1.07083
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Squared 25114 29386 1.1701
708 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Ranked 220.438 209.118 1.05413

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/