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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1230 to 1279 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
154 MYH4 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Measured Subtracted 9035 7279.6 1755.4
RGS19 regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] Ranked Divided 249.663 298.263 1.19466
SLC4A1AP solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] Squared Subtracted 70525.9 52678.7 17847.2
155 CKS2 cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]
CSTF2 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] Divided 126408 89940.5 1.40546
MAGEA11 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] Measured 23693.7 18263 1.29736
MSI1 musashi 1. [refseq;acc:nm_002442] Ranked Subtracted 227.491 199.458 28.033
MYH8 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Measured 9035 7279.6 1755.4
NCBP2L dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Rooted 54.2343 66.7323 12.498
RBM15 putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] Ranked Divided 249.663 298.263 1.19466
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Rooted 55.7423 65.6839 1.17835
156 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 55.1026 67.5701 12.4675
CTNNAL1 catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] Squared 70525.9 52678.7 17847.2
MAGEA2B melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] Measured Divided 23693.7 18263 1.29736
MYH2 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] Subtracted 9035 7279.6 1755.4
RGS20 regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] Ranked Divided 249.663 298.263 1.19466
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Squared 89578.7 125883 1.40528
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] Rooted 56.3447 66.124 1.17356
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Ranked Subtracted 227.491 199.458 28.033
157 no value hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Measured Divided 23693.7 18263 1.29736
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Rooted Subtracted 55.1113 67.5537 12.4424
BRP44 brain protein 44. [swissprot;acc:o95563] Squared Divided 89182.8 125229 1.40418
EIF4G3 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Rooted 52.7582 61.9123 1.17351
HIP1 huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291] Squared Subtracted 76438 58889.7 17548.3
LBX1 transcription factor lbx1. [swissprot;acc:p52954] Ranked Divided 249.663 298.263 1.19466
MYH3 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Measured Subtracted 9035 7279.6 1755.4
NEUROD2 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] Ranked 312 284 28
158 BCAR3 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Rooted Divided 56.3507 66.1252 1.17346
CHD3 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Ranked Subtracted 312 284 28
COL4A3BP goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4] Squared 76360.8 58841.7 17519.1
GPSM2 mosaic protein lgn. [swissprot;acc:p81274] Ranked Divided 249.663 298.263 1.19466
MAGEA6 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Measured 23693.7 18263 1.29736
MYH1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 9035 7279.6 1755.4
PPP1R7 protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712] Rooted 149.397 136.972 12.425
SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Squared Divided 89182.8 125229 1.40418
159 no value myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] Measured Subtracted 9035 7279.6 1755.4
rna-binding protein. [refseq;acc:nm_019027] Rooted Divided 52.7642 61.9019 1.17318
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Subtracted 113.983 101.979 12.004
CDK2AP2 doc-1 related protein (doc-1r). [swissprot;acc:o75956] Ranked 312 284 28
HIP1R huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146] Squared 76296.4 58801.6 17494.8
NDN necdin. [swissprot;acc:q99608] Measured Divided 23693.7 18263 1.29736
RGS17 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] Ranked 249.663 298.263 1.19466
SEPT6 septin 6. [swissprot;acc:q14141] Squared 88953.6 124854 1.40359
160 no value apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576] Rooted 52.7642 61.9019 1.17318
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Squared 173408 242989 1.40126
CCT3 t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368] Subtracted 42788.3 60162.6 17374.3
GNAO1 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] Ranked Divided 249.663 298.263 1.19466
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Rooted Subtracted 43.4291 31.7159 11.7132
MAGED1 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Measured Divided 23693.7 18263 1.29736
MYH7B dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Subtracted 9035 7279.6 1755.4

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/