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 908 to 957 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
227 tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258] Subtracted 0 7879.3 6789.92 1089.38
228 methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] 1 244.126 268.604 24.478
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Divided 226.411 202.088 1.12036
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 0 10303.5 11370.4 1.10355
Subtracted 1066.9
229 60s ribosomal protein l3-like. [swissprot;acc:q92901] 1 242.195 266.663 24.468
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Divided 226.401 202.094 1.12028
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Subtracted 0 15147.2 14091.9 1055.3
poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631] Divided 10899.4 9878.1 1.10339
230 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 1 239.35 267.915 1.11934
interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Subtracted 0 15147.2 14091.9 1055.3
protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] 1 242.694 267.017 24.323
tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208] Divided 0 12364.7 11207.7 1.10323
231 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Subtracted 12447.6 11392.6 1055
likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Divided 1 239.336 267.881 1.11927
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Subtracted 226.411 202.088 24.323
tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702] Divided 0 12364.8 11207.9 1.10322
232 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Subtracted 12448.9 11393.9 1055
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 1 226.401 202.094 24.307
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Divided 0 12394.7 11240.2 1.10271
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 1 239.336 267.879 1.11926
233 60s acidic ribosomal protein p1. [swissprot;acc:p05386] 0 9586.97 10560 1.1015
60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted 1 235.727 259.984 24.257
lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Divided 239.32 267.842 1.11918
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Subtracted 0 10367 9320.25 1046.75
234 40s ribosomal protein s23. [swissprot;acc:p39028] 1 243.944 268.195 24.251
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided 287.41 256.835 1.11905
transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884] 0 16614 18296 1.10124
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 7502.08 6461.83 1040.25
235 28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235] 1 243.944 268.195 24.251
40s ribosomal protein s29. [swissprot;acc:p30054] 0 11035.3 9997.71 1037.59
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 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
236 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Subtracted 252.644 228.42 24.224
keratin associated protein 9.2. [refseq;acc:nm_031961] 0 10551.1 11579.9 1028.8
pp3111 protein. [refseq;acc:nm_022156] Divided 1 227.357 254.15 1.11785
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] 0 15245.4 16788.5 1.10122
237 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] 9984 9067 1.10114
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Subtracted 10551.6 11573.7 1022.1
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] 1 242.011 266.18 24.169
syntaxin 18. [swissprot;acc:q9p2w9] Divided 227.357 254.15 1.11785
238 cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] 0 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
rd protein. [swissprot;acc:p18615] Divided 227.357 254.15 1.11785
239 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Subtracted 243.817 267.962 24.145
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Divided 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
240 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] 1 227.357 254.15 1.11785

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/