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 6662 to 6711 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : Low confidence
Filtered  : 1
Rank
description
red
green
network_comparison
3434 rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] 196.96 194.013 1.01519
3435 mitochondrial glutamate carrier 1. [refseq;acc:nm_024698] 193.374 190.481
3436 phosphoglucomutase-like protein 5 (phosphoglucomutase-related protein) (pgm-rp) (aciculin). [swissprot;acc:q15124] 201.213 198.202
3437 mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2] 199.422 196.439
3438 inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] 196.976 194.028
3439 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 201.282 198.271
3440 endothelial-derived gene 1. [refseq;acc:nm_025205] 198.635 195.663
3441 cpz gene product. [refseq;acc:nm_003652] 201.285 198.273
3442 multiple pdz domain protein. [refseq;acc:nm_003829] 196.978 194.03
3443 cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661] 201.288 198.276
3444 golgi apparatus protein 1 precursor (golgi sialoglycoprotein mg-160) (e-selectin ligand 1) (esl-1) (cysteine-rich fibroblast growth factor receptor) (cfr-1). [swissprot;acc:q92896]
3445 potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 201.282 198.271
3446 ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] 196.979 194.031
3447 elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127]
3448 testis intracellular mediator protein. [refseq;acc:nm_057161] 203.333 200.293 1.01518
3449 enhancer of zeste homolog 1 (enx-2). [swissprot;acc:q92800]
3450 enhancer of zeste homolog 2 (enx-1). [swissprot;acc:q15910]
3451 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 204.036 200.989 1.01516
3452 serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 198.794 195.825
3453 hexokinase, type ii (ec 2.7.1.1) (hk ii) (muscle form hexokinase). [swissprot;acc:p52789] 200.319 197.33 1.01515
3454 presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341] 202.622 199.599
3455 small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 197.533 194.585
3456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 202.709 199.686 1.01514
3457 tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399] 201.597 198.59
3458 hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367] 200.307 197.322 1.01513
3459 phosphoglucomutase (ec 5.4.2.2) (glucose phosphomutase) (pgm). [swissprot;acc:p36871] 201.212 198.213
3460 zinc finger protein with interaction domain. [refseq;acc:nm_006626] 200.298 197.317 1.01511
3461 zinc finger protein bioref. [swissprot;acc:q9hck0] 200.299 197.318
3462 hexokinase type iii (ec 2.7.1.1) (hk iii). [swissprot;acc:p52790] 200.296 197.315
3463 atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964] 202.723 199.708 1.0151
3464 proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] 199.995 197.02
3465 hexokinase d (ec 2.7.1.1) (hexokinase type iv) (hk iv) (hk4) (glucokinase). [swissprot;acc:p35557] 200.291 197.312
3466 isocitrate dehydrogenase [nad] subunit beta, mitochondrial precursor (ec 1.1.1.41) (isocitric dehydrogenase) (nad+-specific icdh). [swissprot;acc:o43837] 200.419 197.437
3467 snare associated protein snapin. [refseq;acc:nm_012437] 201.389 198.396 1.01509
3468 nucleolin (protein c23). [swissprot;acc:p19338] 188.235 185.438 1.01508
3469 zinc finger protein 297b (znf-x). [swissprot;acc:o43298] 200.3 197.326 1.01507
3470 sodium/potassium-transporting atpase beta-3 chain (sodium/potassium- dependent atpase beta-3 subunit) (atpb-3). [swissprot;acc:p54709] 197.125 194.199
3471 sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415] 197.112 194.188 1.01506
3472 limb region 1 protein; limb region 1. [refseq;acc:nm_022458] 204.082 201.054
3473 x/potassium-transporting atpase beta-m chain (x,k-atpase beta-m subunit). [swissprot;acc:q9un42] 197.122 194.197
3474 tyrosyl-dna phosphodiesterase 1; tyrosyl-dna phosphodiesterase. [refseq;acc:nm_018319] 202.946 199.936 1.01505
3475 lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] 204.091 201.067 1.01504
3476 phd finger protein 7 isoform 1. [refseq;acc:nm_016483] 201.206 198.224
3477 vps28 protein homolog. [swissprot;acc:q9uk41] 202.414 205.457 1.01503
3478 heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900] 201.611 198.628 1.01502
3479 brca1-associated ring domain protein 1 (bard-1). [swissprot;acc:q99728] 199.172 196.226 1.01501
3480 aldehyde dehydrogenase family 7 member a1 (ec 1.2.1.3) (antiquitin 1). [swissprot;acc:p49419] 201.442 198.465 1.015
3481 glutathione s-transferase p (ec 2.5.1.18) (gst class-pi) (gstp1-1). [swissprot;acc:p09211] 202.657 199.662
3482 ptd012 protein. [refseq;acc:nm_014039] 202.475 199.484 1.01499
3483 mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439]

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/