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 [...,...].
Filtered green Value Type Gene Rank Interaction Map description network_comparison Network Comparison Type red
Results: HTML CSV LaTeX Showing element 651 to 700 of 77072 in total
Filtered  : 0
green
Value Type
Rank
Interaction Map
description
network_comparison
Network Comparison Type
red
7.14143 Rooted 423 High confidence melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] 1.03078 Divided 6.9282
462 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 0.21323 Subtracted
463 melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
464 melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]
465 melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
466 hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
467 melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
468 melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
469 melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]
470 melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
471 melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
472 melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
473 melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]
474 melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
475 melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
476 melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
477 melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
478 melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
7.16592 Squared 1 cab2. [refseq;acc:nm_033419] 716592 Divided 0.00001
402 7.16592 Subtracted 0
7.2154 103 Low confidence 2.05637 Divided 3.50881
775 3.70659 Subtracted
7.23384 156 williams beuren syndrome chromosome region 21 isoform 1. [refseq;acc:nm_148912] 1.50186 Divided 4.8166
795 2.41724 Subtracted
7.27598 586 sarcoplasmic/endoplasmic reticulum calcium atpase 1 (ec 3.6.3.8) (calcium pump 1) (serca1) (sr ca(2+)-atpase 1) (calcium-transporting atpase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (endoplasmic reticulum class 1/2 ca(2+) atpase). [swissprot;acc:o14983] 1.07676 Divided 6.75729
815 0.51869 Subtracted
7.28011 Rooted 124 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 1.23056 Divided 5.91608
125 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626]
490 acidic leucine-rich nuclear phosphoprotein 32 family member c (tumorigenic protein pp32r1). [swissprot;acc:o43423] 1.36403 Subtracted
491 acidic leucine-rich nuclear phosphoprotein 32 family member d (tumorigenic protein pp32r2). [swissprot;acc:o95626]
7.28282 Squared 139 cln3 protein (battenin) (batten disease protein). [swissprot;acc:q13286] 1.67078 Divided 12.168
770 4.88518 Subtracted
7.31834 Rooted 319 High confidence glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 1.0636 Divided 7.78379
439 0.46545 Subtracted
7.32908 317 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 1.0636 Divided 7.79521
438 0.46613 Subtracted
7.3344 318 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 1.0636 Divided 7.80086
437 0.46646 Subtracted
7.33715 122 mitochondrial 28s ribosomal protein s22 (s22mt) (mrp-s22) (gk002). [swissprot;acc:p82650] 1.22708 Divided 9.00325
126 Low confidence
301 High confidence 1.6661 Subtracted
434 Low confidence
7.34614 24 High confidence microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268] 10.4494 17.7955
29 2.42243 Divided
7.46223 390 williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 1.03475 7.21166
391 williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
392 williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]
457 williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645] 0.25057 Subtracted
458 williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]
459 williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]

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/