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 2325 to 2374 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
291 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Measured Divided 44490.5 36927.5 1.20481
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Squared 59016.1 75486.9 1.27909
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Subtracted 28896.2 36767 7870.8
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Rooted Divided 113.983 101.979 1.11771
292 40s ribosomal protein s15a. [swissprot;acc:p39027] Ranked 241.411 266.414 1.10357
crk-like protein. [swissprot;acc:p46109] Squared Subtracted 28896.2 36767 7870.8
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 234.146 256.627 22.481
neuralized-like. [refseq;acc:nm_004210] Squared Divided 6828.26 8728.66 1.27831
nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384] Measured 4641.09 5588.75 1.20419
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Subtracted 950.561 2108.52 1157.96
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Rooted 66.1064 74.1074 8.001
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Divided 56.48 63.119 1.11755
293 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Ranked 240.782 265.717 1.10356
c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Subtracted 219.421 196.978 22.443
kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Squared Divided 35991.8 46002.9 1.27815
nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2] Measured 4641.09 5588.75 1.20419
proto-oncogene tyrosine-protein kinase abl1 (ec 2.7.1.112) (p150) (c-abl). [swissprot;acc:p00519] Squared Subtracted 28896.2 36767 7870.8
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Rooted Divided 63.0715 56.4506 1.11729
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] Measured Subtracted 4512.19 5655.52 1143.33
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Rooted 66.1064 74.1074 8.001
294 1-acyl-sn-glycerol-3-phosphate acyltransferase beta (ec 2.3.1.51) (1- agp acyltransferase 2) (1-agpat 2) (lysophosphatidic acid acyltransferase-beta) (lpaat-beta) (1-acylglycerol-3-phosphate o- acyltransferase 2). [swissprot;acc:o15120] Squared Divided 30826.5 39383.9 1.2776
brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Ranked 240.782 265.717 1.10356
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] Measured 22515.5 18702.6 1.20387
crk-like protein. [swissprot;acc:p46109] Rooted Subtracted 66.1064 74.1074 8.001
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Ranked 219.421 196.978 22.443
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Squared 28896.2 36767 7870.8
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Rooted Divided 59.0296 65.951 1.11725
small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] Measured Subtracted 4512.19 5655.52 1143.33
295 1-acyl-sn-glycerol-3-phosphate acyltransferase alpha (ec 2.3.1.51) (1- agp acyltransferase 1) (1-agpat 1) (lysophosphatidic acid acyltransferase-alpha) (lpaat-alpha) (1-acylglycerol-3-phosphate o- acyltransferase 1) (g15 protein). [swissprot;acc:q99943] Squared Divided 30807.7 39351.7 1.27733
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] Measured Subtracted 5720.25 4577.5 1142.75
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Ranked 219.421 196.978 22.443
multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904] Divided 223.273 202.423 1.103
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Squared Subtracted 28896.2 36767 7870.8
proto-oncogene tyrosine-protein kinase fyn (ec 2.7.1.112) (p59-fyn) (syn) (slk). [swissprot;acc:p06241] Rooted 66.1064 74.1074 8.001
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Measured Divided 13261.9 11017.8 1.20368
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Rooted 59.029 65.9421 1.11711
296 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 63.0663 56.4667 1.11688
grb2-related adaptor protein 2 (gads protein) (growth factor receptor binding protein) (grblg) (grf40 adaptor protein) (grf-40) (grb-2-like protein) (grb2l) (grbx) (p38) (hematopoietic cell-associated adaptor protein grpl) (adapter protein grid) (sh3-sh2-sh3 adaptor mona). [swissprot;acc:o75791] Squared Subtracted 28896.4 36766.8 7870.4
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Ranked 219.421 196.978 22.443
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Divided 241.282 266.12 1.10294
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Measured Subtracted 3620.77 4763.34 1142.57
proto-oncogene tyrosine-protein kinase fgr (ec 2.7.1.112) (p55-fgr) (c-fgr). [swissprot;acc:p09769] Rooted 66.1064 74.1074 8.001
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Measured Divided 4911.81 5909.18 1.20306
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Squared 28878.8 36783.5 1.27372
297 60s ribosomal protein l7. [swissprot;acc:p18124] Ranked 235.727 259.984 1.1029
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880] Squared Subtracted 28900.8 36762.6 7861.8
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Measured 3620.77 4763.34 1142.57
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Divided 4911.81 5909.18 1.20306
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Ranked Subtracted 219.421 196.978 22.443
ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Squared Divided 14247.4 18142.1 1.27336

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/