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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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 1825 to 1874 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Value Type
red
network_comparison
green
229 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Divided Ranked 226.401 1.12028 202.094
EPB41L2 band 4.1-like protein 2 (generally expressed protein 4.1) (4.1g). [swissprot;acc:o43491] Subtracted Squared 45986 10790.1 56776.1
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Divided Rooted 137.446 1.13758 120.823
MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Squared 42411.6 1.31573 55802.1
MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Measured 9035 1.24114 7279.6
MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Subtracted Rooted 95.0526 9.732 85.3206
RPL3L 60s ribosomal protein l3-like. [swissprot;acc:q92901] Ranked 242.195 24.468 266.663
SGTA small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Measured 10434.4 1411.8 11846.2
230 CSRP1 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] Divided Ranked 239.35 1.11934 267.915
EIF1 protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567] Subtracted 242.694 24.323 267.017
MAPK11 mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Measured 9649.61 1403.89 11053.5
MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Divided 9035 1.24114 7279.6
MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Subtracted Rooted 95.0526 9.732 85.3206
NDN necdin. [swissprot;acc:q99608] Divided 137.446 1.13758 120.823
SDF4 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Subtracted Squared 45987 10790.1 56777.1
SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Divided 42411.6 1.31573 55802.1
231 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Measured 9035 1.24114 7279.6
DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Squared 42411.6 1.31573 55802.1
LGALS9 galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Subtracted 45960.8 10788.8 56749.6
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Divided Rooted 137.446 1.13758 120.823
MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 95.0526 9.732 85.3206
SH2D3C sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Ranked 226.411 24.323 202.088
SHCBP1 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] Divided 239.336 1.11927 267.881
SPHK1 sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1] Subtracted Measured 9649.61 1403.89 11053.5
232 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Ranked 226.401 24.307 202.094
CSRP2 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] Divided 239.336 1.11926 267.879
DLC1 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Squared 42411.6 1.31573 55802.1
DPAGT1 udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5] Subtracted Measured 9649.61 1403.89 11053.5
HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Squared 41502.9 10666.1 30836.8
MAGEF1 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Divided Rooted 137.446 1.13758 120.823
MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 95.0526 9.732 85.3206
MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Divided Measured 9035 1.24114 7279.6
233 no value 60s ribosomal protein l7. [swissprot;acc:p18124] Subtracted Ranked 235.727 24.257 259.984
CSRP3 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] Divided 239.32 1.11918 267.842
DLC1 rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1] Subtracted Measured 9649.61 1403.89 11053.5
HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Squared 41502.9 10666.1 30836.8
MAGEB6B melanoma antigen, family b, 6. [refseq;acc:nm_173523] Divided Rooted 137.446 1.13758 120.823
MAPKAPK2 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Squared 42411.6 1.31573 55802.1
MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted Rooted 95.0526 9.732 85.3206
MYH13 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] Divided Measured 9035 1.24114 7279.6
234 no value melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358] Rooted 137.446 1.13758 120.823
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Subtracted 95.0526 9.732 85.3206
CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Divided Ranked 287.41 1.11905 256.835
CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Squared 42411.6 1.31573 55802.1
HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Subtracted 41502.9 10666.1 30836.8
MAPKAPK2 map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137] Measured 9649.61 1403.89 11053.5
RPS23 40s ribosomal protein s23. [swissprot;acc:p39028] Ranked 243.944 24.251 268.195
RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] Divided Measured 5181.2 1.23728 6410.58
235 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
CHRNA6 neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825] Subtracted 9649.61 1403.89 11053.5

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/