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 2130 to 2179 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
267 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] Squared 1 26157.6 20236.2 1.29261
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] 0 181.291 144.478 1.2548
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Measured 1 14021.4 11523 1.21682
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Rooted 0 12.9585 14.1963 1.09552
transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268] Ranked 8054.34 8772.02 1.0891
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Rooted 1 66.1064 74.1073 1.12103
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452] Measured 0 1475.05 1312.91 1.1235
268 cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] 1 24473.9 20127.8 1.21593
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Ranked 271.016 244.167 1.10996
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Measured 0 604.529 538.094 1.12346
laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] Squared 1 26157.6 20236.2 1.29261
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Ranked 0 14257.4 13134.5 1.08549
protein cgi-147. [swissprot;acc:q9y3e5] Squared 75129.2 94178 1.25355
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 1 66.1064 74.1074 1.12103
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] 0 13.0249 14.2577 1.09465
269 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Measured 1217.92 1367.83 1.12309
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Squared 4121.56 5159.2 1.25176
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Ranked 1 241.373 267.352 1.10763
ischemia/reperfusion inducible protein. [refseq;acc:nm_024640] 0 12463.5 11482.6 1.08542
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Rooted 90.4079 98.9265 1.09422
thymic stromal co-transporter. [refseq;acc:nm_033051] Squared 1 26157.6 20236.2 1.29261
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted 66.1064 74.1074 1.12103
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured 4590.18 5575.52 1.21466
270 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Squared 0 2569.37 3201.81 1.24615
crk-like protein. [swissprot;acc:p46109] Rooted 1 66.1064 74.1074 1.12103
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Ranked 0 10735.1 9891.37 1.0853
fad synthetase. [refseq;acc:nm_025207] 1 241.373 267.352 1.10763
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 1.21358
ribosomal protein l10-like protein. [refseq;acc:nm_080746] 0 1217.96 1367.88 1.12309
transcription factor iib. [refseq;acc:nm_013242] Squared 1 64739.9 50300.6 1.28706
zinc finger protein 277. [swissprot;acc:q9nrm2] Rooted 0 90.4079 98.9265 1.09422
271 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] Ranked 1 241.373 267.352 1.10763
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Measured 2554.89 3093.78 1.21092
guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148] Squared 0 92.5367 74.2791 1.2458
histone h4. [swissprot;acc:p02304] Measured 21773.1 24446.3 1.12278
microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650] Rooted 17.4356 19.0526 1.09274
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Ranked 10735.1 9891.37 1.0853
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Rooted 1 66.1064 74.1073 1.12103
splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872] Squared 64739.9 50300.6 1.28706
272 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 0 4225.7 5255.44 1.24369
60s ribosomal protein l15. [swissprot;acc:p39030] Measured 846.216 753.793 1.12261
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] Squared 1 36563.7 46971.1 1.28464
chromodomain y-like protein 2. [refseq;acc:nm_152342] Rooted 0 33.0227 30.2263 1.09252
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Measured 1 3858.52 4669.27 1.21012
ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Ranked 241.373 267.352 1.10763
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 66.1064 74.1074 1.12103
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Ranked 0 7163.55 7759.61 1.08321
273 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Squared 4224.07 5253.37 1.24367
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252] Ranked 1 241.373 267.352 1.10763
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Measured 3199.4 3870.8 1.20985

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/