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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 762 to 811 of 66312 in total
Filtered  : 1
Rank
Hugo
Value Type
description
Network Comparison Type
Interaction Map
red
green
network_comparison
48 PAPOLG Squared poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Subtracted High confidence 210199 136638 73561
PBK Rooted t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Divided 27.7254 44.0299 1.58807
RAB11FIP3 Measured eferin. [swissprot;acc:o75154] Subtracted Low confidence 7407.56 8696.7 1289.14
Rooted 73.6221 81.4944 7.8723
TOB1 Ranked tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] High confidence 350 290 60
TRO Squared trophinin. [swissprot;acc:q12816] Divided Low confidence 82347.8 61881.5 1.33073
WDR33 Measured wd-repeat protein wdc146. [swissprot;acc:q9c0j8] Subtracted High confidence 24806.9 20369.9 4437
49 no value Squared homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided Low confidence 122475 159767 1.30449
ARRB2 Ranked beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] High confidence 133 105 1.26667
CPEB3 Rooted cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Subtracted Low confidence 48.8531 56.7071 7.854
CPSF1 Measured cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570] High confidence 24806.9 20369.9 4437
CSTF3 Squared cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326] 201896 131906 69990
DAB2IP Ranked dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 350 290 60
FOSL1 Rooted fos-related antigen 1 (fra-1). [swissprot;acc:p15407] Divided Low confidence 66.6623 75.3751 1.1307
KHDRBS3 kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] High confidence 27.7254 44.0299 1.58807
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Subtracted 137.446 120.823 16.623
MAGEA4 Squared melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365] Low confidence 82347.8 61881.5 20466.3
MAP1LC3B Measured microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8] Divided 13470.1 11654.4 1.1558
NEUROD6 neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] High confidence 779.167 1390.33 1.78438
SEPT4 septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Subtracted Low confidence 11141.5 12351.1 1209.6
STAMBPL1 Squared associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided High confidence 28994.2 17134.8 1.69212
TBX19 Ranked t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806] Low confidence 225.438 202.569 1.11289
Subtracted 22.869
50 no value Squared homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence 173408 242989 69581
melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355] Low confidence 82347.8 61881.5 20466.3
ARRB1 Ranked beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Divided High confidence 133 105 1.26667
CHMP2A Squared putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 28994.2 17134.8 1.69212
CPD Rooted carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [swissprot;acc:o75976] Low confidence 202.235 178.965 1.13003
CPEB4 Ranked cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Subtracted High confidence 350 290 60
Rooted Low confidence 48.8781 56.7253 7.8472
CPSF2 Measured cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0] High confidence 24473.9 20127.8 4346.1
HOXB4 Squared homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Divided Low confidence 122475 159767 1.30449
JPH3 Ranked junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 234.802 260.98 1.11149
KHDRBS1 Rooted kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] High confidence 27.7254 44.0299 1.58807
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Subtracted 137.446 120.823 16.623
MAP1LC3A Measured microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492] Divided Low confidence 13466.8 11652.4 1.15571
NDUFA12 Ranked nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Subtracted 233.134 210.267 22.867
NEUROD1 Measured neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] Divided High confidence 779.167 1390.33 1.78438
VASP vasodilator-stimulated phosphoprotein (vasp). [swissprot;acc:p50552] Subtracted Low confidence 12768 11571.4 1196.6
51 no value ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08]
Rooted hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] High confidence 137.446 120.823 16.623
CPEB3 Ranked cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 350 290 60
FIP1L1 Measured fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 23640.2 19479.8 4160.4
GBAS Ranked nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Low confidence 249.709 226.944 22.765
Rooted Divided 55.0884 62.0722 1.12677
GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted 62.7951 70.575 7.7799
HOXB4 Squared homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] High confidence 173408 242989 69581
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Divided Low confidence 122475 159767 1.30449
JPH2 Ranked junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] 234.802 260.98 1.11149
KHDRBS2 Rooted kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] High confidence 27.7254 44.0299 1.58807

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
- Hugo is the HGNC identifier if it exists
- 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/