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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 [...,...].
Gene Rank Value Type description Filtered Network Comparison Type Interaction Map green red network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 77072 in total
Rank
Value Type
description
Filtered
Network Comparison Type
Interaction Map
green
red
network_comparison
4 Measured homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 Divided Low confidence 89 0.00001 8900000
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] High confidence
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 1 Low confidence 543.5 2399.5 4.4149
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 Subtracted High confidence 21730 18704 3026
Ranked cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [swissprot;acc:q00534] 1 Divided Low confidence 330 223 1.47982
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] High confidence 28 15 1.86667
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Subtracted Low confidence 330 223 107
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 Divided High confidence 21883 8906 2.45711
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] Subtracted Low confidence 14977 5865 9112
neurogenic locus notch homolog protein 2 precursor (notch 2) (hn2). [swissprot;acc:q04721] Divided 20617 9607 2.14604
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] Subtracted High confidence 21888 11525 10363
rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6] 1 232 337 105
Squared cytochrome c oxidase polypeptide viic, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p15954] 0 Low confidence 295570 273831 21739
cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418] 1 High confidence 263351 407289 143938
guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4] 0 Divided Low confidence 0.823905 0.00001 82390.5
hbs1-like. [refseq;acc:nm_006620] 1 High confidence 115.48 1596.92 13.8285
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] Low confidence 69.9153 1362.75 19.4914
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Subtracted 473408 332411 140997
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] 0 Divided High confidence 2.81207 0.00001 281207
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Subtracted 105900 75446.7 30453.3
Rooted hbs1-like. [refseq;acc:nm_006620] 1 Divided 26.4292 50.9657 1.92839
Subtracted 24.5365
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] 0 Divided Low confidence 9.43398 0.00001 943398
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 1 23.3131 48.9847 2.10117
Subtracted 25.6716
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] 0 0 19.0788 19.0788
mln 64 protein (star-related lipid transfer protein 3) (stard3) (start domain-containing protein 3) (cab1 protein). [swissprot;acc:q14849] High confidence 7.61577 29.3087 21.6929
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Divided 10.4403 0.00001 1044030
5 Measured cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] 1 Subtracted 33356.5 41482.5 8126
histone h4. [swissprot;acc:p02304] 0 24446.3 21773.1 2673.2
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Divided 89 0.00001 8900000
jumonji protein. [swissprot;acc:q92833] Low confidence 17.5166 1751660
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 High confidence 339.5 1153.5 3.39764
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] 0 Subtracted Low confidence 2740.13 485.286 2254.84
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] 1 Divided 2113.5 736.5 2.86965
vitelliform macular dystrophy 2-like protein 2. [refseq;acc:nm_153274] Subtracted 43503.3 36469.3 7034
Ranked cytohesin 4. [swissprot;acc:q9uia0] Divided High confidence 28 15 1.86667
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 0 Subtracted Low confidence 13216 22286 9070
lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [swissprot;acc:p13473] 1 Divided 330 223 1.47982
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Subtracted 240 318 78
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 0 High confidence 21888 11525 10363
ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855] Divided 11965.7 5510.5 2.17144
ubiquitously transcribed y chromosome tetratricopeptide repeat protein (ubiquitously transcribed tpr protein on the y chromosome). [swissprot;acc:o14607] Low confidence 19873 10889.4 1.82499
xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266] 1 Subtracted High confidence 309 212 97
Squared carbohydrate (n-acetylglucosamine 6-o) sulfotransferase 6; macular dystrophy, corneal, 1; carbohydate sulfotransferase 6; corneal n-acetylglucosamine 6-sulfotransferase. [refseq;acc:nm_021615] 0 Divided Low confidence 0.00001 0.324024 32402.4
cytohesin 4. [swissprot;acc:q9uia0] 1 Subtracted High confidence 263351 407289 143938
ena/vasodilator stimulated phosphoprotein-like protein (ena/vasp-like protein). [swissprot;acc:q9ui08] 0 Low confidence 59791.4 40110.9 19680.5
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Divided High confidence 1.87479 0.00001 187479
junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2] 1 27.2805 314.926 11.544
oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [swissprot;acc:q9bzf3] Low confidence 1057.25 128.386 8.23493

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/