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.


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Rank Gene description Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1051 to 1100 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
526 histone h2b. [refseq;acc:nm_175055] Subtracted 247.47 233.441 14.029
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Divided 250.538 234.401 1.06884
527 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] 248.56 232.579 1.06871
histone h2b.s (h2b/s). [swissprot;acc:p57053] Subtracted 247.47 233.441 14.029
528 histone h2b.d (h2b/d). [swissprot;acc:q99877]
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Divided 222.146 237.393 1.06864
529 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Subtracted 247.47 233.441 14.029
530 testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Divided 227.483 212.994 1.06803
531 histone h2b.e (h2b/e). [swissprot;acc:q99879] Subtracted 247.47 233.441 14.029
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Divided 223.356 209.149 1.06793
532 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Subtracted 112 126 14
zinc finger-like protein 9. [refseq;acc:nm_033414] Divided 250.942 235.004 1.06782
533 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Subtracted 58 44 14
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Divided 250.942 235.004 1.06782
534 guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915]
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Subtracted 58 44 14
535 dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Divided 236.662 252.708 1.0678
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] Subtracted 112 126 14
536 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Divided 242.531 227.136 1.06778
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] Subtracted 112 126 14
537 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 10 24
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Divided 229.803 215.301 1.06736
538 dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436] 237.627 253.604 1.06724
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Subtracted 58 44 14
539 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 112 126
protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] Divided 236.964 252.86 1.06708
540 pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Subtracted 58 44 14
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Divided 222.156 208.201 1.06703
541 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] Subtracted 112 126 14
542 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Divided 222.156 208.201 1.06703
myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] Subtracted 112 126 14
543 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] Divided 222.156 208.201 1.06703
544 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] Subtracted 112 126 14
inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566] Divided 222.156 208.201 1.06703
545 eukaryotic translation initiation factor 6 (eif-6) (b4 integrin interactor) (cab) (p27(bbp)) (b(2)gcn homolog). [swissprot;acc:p56537] 248.866 233.287 1.06678
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Subtracted 58 44 14
546 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 112 126
wiskott-aldrich syndrome protein (wasp). [swissprot;acc:p42768] Divided 207.222 194.262 1.06671
547 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Subtracted 234.106 248.104 13.998
proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108] Divided 207.26 194.346 1.06645
548 selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] Subtracted 222.156 208.201 13.955
tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684] Divided 207.26 194.346 1.06645
549 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632] Subtracted 222.156 208.201 13.955
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Divided 207.26 194.346 1.06645
550 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] Subtracted 222.156 208.201 13.955
tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631] Divided 207.26 194.346 1.06645

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/