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 [...,...].
Gene Value Type Rank description Network Comparison Type Interaction Map Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 551 to 600 of 77072 in total
Value Type  : Measured
Rank
description
Network Comparison Type
Interaction Map
Filtered
red
network_comparison
green
69 tubulointerstitial nephritis antigen. [refseq;acc:nm_014464] Divided Low confidence 0 129 1.82979 70.5
zinc finger protein 223. [swissprot;acc:q9uk11] Subtracted 2354.34 383.13 1971.21
70 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Divided High confidence 1 6475.5 1.59177 10307.5
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938] Subtracted 0 570 431 139
importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292] Divided 607 1.75947 1068
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Subtracted Low confidence 1 10499 1016.8 11515.8
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] High confidence 17738.5 3742.8 13995.7
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Divided Low confidence 0 167.73 1.82368 305.886
y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01] 1 6991.78 1.12253 7848.45
zinc finger imprinted 3. [swissprot;acc:q96pe6] Subtracted 0 2354.3 383.13 1971.17
71 cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5] Divided 1 6991.78 1.12253 7848.45
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Subtracted 5339.5 1012.9 6352.4
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Divided High confidence 4556.78 1.54716 2945.26
serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] Subtracted 17738.5 3742.8 13995.7
tubby protein homolog. [swissprot;acc:p50607] 0 3797.57 430.7 4228.27
ubiquitin protein ligase. [refseq;acc:nm_130466] Divided 620 1.75762 352.75
zinc finger protein 233. [refseq;acc:nm_181756] Subtracted Low confidence 2354.06 383.11 1970.95
zona pellucida sperm-binding protein 3 precursor (zona pellucida glycoprotein zp3) (zona pellucida protein c) (sperm receptor) (zp3a/zp3b). [swissprot;acc:p21754] Divided 270.432 1.80287 150.001
72 60s ribosomal protein l21. [swissprot;acc:p46778] High confidence 572 1.73441 992.083
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] Subtracted 1 17710.9 3733.2 13977.7
b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2] Divided Low confidence 0 271.129 1.79562 150.995
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] Subtracted High confidence 679.449 427.431 1106.88
serine/threonine-protein kinase mak (ec 2.7.1.-) (male germ cell- associated kinase). [swissprot;acc:p20794] Low confidence 1 9631.47 1001.53 10633
solute carrier family 7 (cationic amino acid transporter, y+ system), member 6. [refseq;acc:nm_003983] Divided 6991.78 1.12253 7848.45
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] High confidence 4556.79 1.54715 2945.28
zinc finger protein 334. [swissprot;acc:q9hcz1] Subtracted Low confidence 0 2354.02 383.11 1970.91
73 eukaryotic translation initiation factor 4b (eif-4b). [swissprot;acc:p23588] Divided 1 6991.78 1.12253 7848.45
intestinal cell kinase isoform a; mak-related kinase; serine/threonine protein kinase. [refseq;acc:nm_014920] Subtracted 9623.55 997.75 10621.3
krab zinc finger protein hzf26 (fragment). [sptrembl;acc:q9bze6] 0 2353.9 383.1 1970.8
protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236] Divided High confidence 65.2968 1.73233 37.693
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] Subtracted 1965.47 424.22 2389.69
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Divided 1 4556.83 1.54711 2945.38
serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [swissprot;acc:p36873] Subtracted 22268.8 3708.4 18560.4
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] Divided Low confidence 0 688.436 1.78524 385.626
74 arf gtpase-activating protein. [refseq;acc:nm_133446] 66 1.78378 37
b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251] 1 6991.78 1.12253 7848.45
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820] High confidence 0 501.151 1.71473 859.34
glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488] Subtracted 14267.5 421.3 14688.8
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] 1 20446.1 3690.3 24136.4
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Low confidence 11285.3 966.8 10318.5
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Divided High confidence 4556.99 1.54694 2945.8
zinc finger protein 195. [swissprot;acc:o14628] Subtracted Low confidence 0 2353.86 383.1 1970.76
75 60s ribosomal protein l21. [swissprot;acc:p46778] High confidence 572 420.083 992.083
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Low confidence 1 11285.3 966.8 10318.5
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] High confidence 20446.1 3690.3 24136.4
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Divided 1920.75 1.5137 2907.43
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 0 1586.07 1.71412 925.298
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Low confidence 1 11616 1.11418 12942.3
up-regulated in liver cancer 1; similar to development- and differentiation-enhancing factor 2. [refseq;acc:nm_017707] 0 66 1.78378 37
zinc finger protein 230 (zinc finger protein fdzf2). [swissprot;acc:q9uie0] Subtracted 2353.79 383.09 1970.7

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/