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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 9586 to 9635 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
697 ferritin heavy chain (ferritin h subunit). [swissprot;acc:p02794] Ranked Divided 220.444 209.113 1.05419
Subtracted 11.331
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] Measured 5768.32 6434.78 666.46
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [swissprot;acc:p04181] Squared Divided 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
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Squared Subtracted 19556 23891.8 4335.8
698 armet protein precursor (arginine-rich protein). [swissprot;acc:p55145] Measured Divided 7101.95 7949.85 1.11939
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Ranked Subtracted 220.438 209.118 11.32
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Rooted Divided 128.909 120.173 1.0727
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Squared Subtracted 19546.1 23881.6 4335.5
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Measured 5768.32 6434.78 666.46
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Rooted 100.169 95.6772 4.4918
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Ranked Divided 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 modulator of immune recognition. [refseq;acc:nm_145021] Measured Subtracted 5768.32 6434.78 666.46
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Ranked Divided 220.438 209.118 1.05413
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Subtracted 11.32
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Squared 25626.4 29950.3 4323.9
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113] Measured Divided 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
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Rooted Subtracted 100.169 95.6772 4.4918
700 40s ribosomal protein s28. [swissprot;acc:p25112] Measured Divided 7161.14 8015.92 1.11936
5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Rooted Subtracted 66.9737 71.4637 4.49
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973] Divided 57.0263 61.1552 1.0724
atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Squared Subtracted 25626.4 29950.3 4323.9
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 11.32
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6] Divided 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
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Measured Subtracted 5768.32 6434.78 666.46
701 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Rooted 66.9738 71.4638 4.49
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Squared Divided 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
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Measured Subtracted 5768.32 6434.78 666.46
guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Squared 25626.4 29950.3 4323.9
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Measured Divided 7802.31 8731.82 1.11913
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Ranked Subtracted 220.438 209.118 11.32
ras-related protein rab-37. [swissprot;acc:q96ax2] Rooted Divided 51.4945 48.0189 1.07238
702 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Subtracted 66.9736 71.4636 4.49
limkain b1. [refseq;acc:nm_019081] Ranked 220.438 209.118 11.32
putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865] Divided 1.05413
ras-related protein rab-26. [swissprot;acc:q9ulw5] Rooted 51.4945 48.0189 1.07238
ribonuclease hi large subunit (ec 3.1.26.-) (rnase hi large subunit) (rnase h(35)) (ribonuclease h2) (rnase h2). [swissprot;acc:o75792] Squared Subtracted 25727.7 30046.7 4319
sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Measured Divided 7067.46 7909.27 1.11911
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Subtracted 5549.2 6215.42 666.22
vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Squared Divided 25114 29386 1.1701
703 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Rooted Subtracted 66.9737 71.4637 4.49
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Divided 51.4945 48.0189 1.07238
limkain b1. [refseq;acc:nm_019081] 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/