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.


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

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/