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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 5158 to 5207 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
645 nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8] Squared Divided 22722.5 26786.5 1.17885
orphan nuclear receptor tr2. [swissprot;acc:p13056] Subtracted 29904.9 34332.5 4427.6
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387] Rooted Divided 63.1463 68.1044 1.07852
646 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Squared 27898 32866.2 1.17808
creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540] Subtracted 58303.5 53878.8 4424.7
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Measured 7273.78 7991.72 717.94
dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4] Rooted Divided 63.1463 68.1044 1.07852
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Measured 4019.88 4522.61 1.12506
histone h2b.d (h2b/d). [swissprot;acc:q99877] Rooted Subtracted 50.6084 55.2961 4.6877
short coiled-coil protein; short coiled coil protein. [refseq;acc:nm_032547] Ranked Divided 216.731 229.549 1.05914
single-minded homolog 1. [swissprot;acc:p81133] Subtracted 226.497 214.355 12.142
647 atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565] Squared 25852.2 30258.6 4406.4
calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Rooted Divided 64.5657 69.6237 1.07834
cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858] Squared 33384.2 39324.9 1.17795
dynein light chain 2. [refseq;acc:nm_080677] Ranked 216.731 229.549 1.05914
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Rooted Subtracted 50.6084 55.2961 4.6877
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260] Ranked 214.257 202.125 12.132
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Measured 2411.93 1695.45 716.48
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 5167.88 4594.43 1.12481
648 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Subtracted 2414.22 1698.12 716.1
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482] Ranked 214.257 202.132 12.125
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Squared 6300.2 10703.5 4403.3
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Ranked Divided 218.227 206.078 1.05895
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Squared 29174 34363.5 1.17788
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Measured 5248.07 5901.72 1.12455
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Rooted 64.5685 69.6269 1.07834
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Subtracted 50.6084 55.2961 4.6877
649 dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [swissprot;acc:p27695] Squared 31445.2 35847.4 4402.2
eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Ranked Divided 233.725 220.751 1.05877
grancalcin. [swissprot;acc:p28676] Rooted 64.5659 69.624 1.07834
histone h2b.e (h2b/e). [swissprot;acc:q99879] Subtracted 50.6084 55.2961 4.6877
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269] Ranked 214.257 202.132 12.125
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Measured 2414.77 1698.75 716.02
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Squared Divided 29173.8 34362.7 1.17786
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Measured 5248.07 5901.72 1.12455
650 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Squared Subtracted 15734.4 20126.8 4392.4
chromodomain y-like protein 2. [refseq;acc:nm_152342] Divided 29016.1 34169.2 1.17759
golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Measured 8362.81 9402.7 1.12435
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274] Ranked Subtracted 214.257 202.135 12.122
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Rooted 50.2554 45.5687 4.6867
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Measured 2416.53 1700.8 715.73
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Rooted Divided 64.566 69.6241 1.07834
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Ranked 228.986 216.276 1.05877
651 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] Rooted Subtracted 50.2554 45.5688 4.6866
bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Ranked Divided 233.725 220.751 1.05877
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Measured 5168.43 4597.44 1.1242
gamma-aminobutyric-acid receptor gamma-3 subunit precursor (gaba(a) receptor). [swissprot;acc:q99928] Ranked Subtracted 214.256 202.139 12.117
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Measured 4509.54 5223.95 714.41
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Rooted Divided 64.5685 69.6269 1.07834
testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] Squared 29012.2 34163.9 1.17757

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/