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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1875 to 1924 of 19268 in total
Value Type  : Ranked
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
green
network_comparison
235 elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720] Divided High confidence 0 14554.5 16027.9 1.10123
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] 1 227.357 254.15 1.11785
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Subtracted Low confidence 0 12808.6 11717.8 1090.8
u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] 1 202.727 193.31 9.417
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Divided 202.654 193.53 1.04715
zinc finger protein 157 (hzf22). [swissprot;acc:p51786] 0 4255.83 4852.69 1.14025
236 dual oxidase 1 precursor; nadph thyroid oxidase 1; flavoprotein nadph oxidase; nicotinamide adenine dinucleotide phosphate oxidase. [refseq;acc:nm_017434] Subtracted 1 210.487 201.076 9.411
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] High confidence 252.644 228.42 24.224
keratin associated protein 9.2. [refseq;acc:nm_031961] 0 10551.1 11579.9 1028.8
peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Divided Low confidence 1 212.056 202.524 1.04707
pp3111 protein. [refseq;acc:nm_022156] High confidence 227.357 254.15 1.11785
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 0 15245.4 16788.5 1.10122
tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Subtracted Low confidence 13627.5 12538.5 1089
zinc finger protein 92 (zinc finger protein htf12) (fragment). [swissprot;acc:q03936] Divided 4255.83 4852.69 1.14025
237 alanine-glyoxylate aminotransferase 2-like 1. [refseq;acc:nm_031279] Subtracted 12706.6 13789.7 1083.1
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Divided High confidence 9984 9067 1.10114
diacylglycerol o-acyltransferase 1 (ec 2.3.1.20) (diglyceride acyltransferase) (acat related gene product 1). [swissprot;acc:o75907] Subtracted Low confidence 1 210.443 201.051 9.392
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] High confidence 0 10551.6 11573.7 1022.1
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 1 242.011 266.18 24.169
single-minded homolog 1. [swissprot;acc:p81133] Divided Low confidence 212.056 202.524 1.04707
syntaxin 18. [swissprot;acc:q9p2w9] High confidence 227.357 254.15 1.11785
zinc finger protein 211 (zinc finger protein c2h2-25). [swissprot;acc:q13398] Low confidence 0 4255.83 4852.69 1.14025
238 ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9] Subtracted 9978.85 11061.5 1082.65
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Divided High confidence 12677.7 13941.7 1.0997
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Subtracted 10551.6 11573.7 1022.1
metastasis-associated protein mta1. [swissprot;acc:q13330] 1 252.512 228.356 24.156
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Divided Low confidence 200.699 191.678 1.04706
rd protein. [swissprot;acc:p18615] High confidence 227.357 254.15 1.11785
similar to zinc finger protein 85 (zinc finger protein hpf4) (htf1). [refseq;acc:nm_145287] Low confidence 0 4256.39 4853.29 1.14024
tensin. [refseq;acc:nm_022648] Subtracted 1 215.258 205.872 9.386
239 60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914] 0 12003.2 10927.4 1075.8
dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] High confidence 1 243.817 267.962 24.145
dual oxidase 2 precursor; dual oxidase-like domains 2; nicotinamide adenine dinucleotide phosphate oxidase; flavoprotein nadph oxidase; nadph thyroid oxidase 2; nadh/nadph thyroid oxidase p138-tox; nadph oxidase/peroxidase duox2. [refseq;acc:nm_014080] Divided Low confidence 210.504 201.086 1.04684
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] High confidence 227.357 254.15 1.11785
keratin associated protein 1.5. [refseq;acc:nm_031957] Subtracted 0 10551.6 11573.7 1022.1
mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] Divided 8907.41 9795.36 1.09969
nadph oxidase, ef hand calcium-binding domain 5. [refseq;acc:nm_024505] Subtracted Low confidence 1 210.415 201.035 9.38
similar to zinc finger protein 136. [refseq;acc:nm_145295] Divided 0 4256.39 4853.29 1.14024
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] High confidence 1 227.357 254.15 1.11785
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Subtracted 252.39 228.297 24.093
cytochrome b-245 heavy chain (p22 phagocyte b-cytochrome) (neutrophil cytochrome b, 91 kda polypeptide) (cgd91-phox) (gp91-phox) (heme binding membrane glycoprotein gp91phox) (cytochrome b(558) beta chain) (superoxide-generating nadph oxidase heavy chain subunit). [swissprot;acc:p04839] Low confidence 210.414 201.035 9.379
cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954] 0 7975.69 9049.44 1073.75
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided 1 162.755 155.476 1.04682
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Subtracted High confidence 0 10551.6 11573.7 1022.1
methyltransferase like 2. [refseq;acc:nm_018396] Divided 17946 16326 1.09923
similar to dna-binding protein; zinc finger protein 253. [refseq;acc:nm_145297] Low confidence 4256.39 4853.29 1.14024
241 atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] High confidence 1 227.357 254.15 1.11785
epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Subtracted 241.892 265.96 24.068
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided Low confidence 162.755 155.476 1.04682
keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966] Subtracted High confidence 0 10551.6 11573.7 1022.1

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/