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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1075 to 1124 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
Network Comparison Type
red
green
network_comparison
135 CLSTN2 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] Squared Subtracted 71033.4 95440.2 24406.8
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked Divided 350 290 1.2069
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Subtracted 263.215 231.407 31.808
GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] Squared Divided 81888.8 56306.5 1.45434
JUNB transcription factor jun-b. [swissprot;acc:p17275] Measured Subtracted 5579.18 7488.4 1909.22
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Rooted Divided 54.935 66.6101 1.21253
136 no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] Squared 81888.8 56306.5 1.45434
ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] Rooted 41.8357 50.6469 1.21061
CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Subtracted 49.2923 62.3969 13.1046
CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Measured 12787.6 10880.5 1907.1
CLSTN3 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] Squared 71030.1 95434.8 24404.7
CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked Divided 350 290 1.2069
FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Subtracted 263.215 231.407 31.808
NFYC nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952] Measured Divided 3620.77 4763.34 1.31556
137 CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Rooted Subtracted 49.2925 62.397 13.1045
CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Measured 12786.6 10879.9 1906.7
CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared Divided 81606.8 56215.8 1.45167
FOXP3 forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Ranked Subtracted 263.191 231.394 31.797
MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Rooted Divided 54.9787 66.2416 1.20486
NFYA ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511] Measured 3620.77 4763.34 1.31556
RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked 350 290 1.2069
SGTA small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] Squared Subtracted 69549 92953.5 23404.5
138 CACNG4 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Rooted 49.293 62.3973 13.1043
HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Squared 70739 93908.8 23169.8
KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured Divided 2755.15 2094.3 1.31555
MSI1 musashi 1. [refseq;acc:nm_002442] Rooted 54.9787 66.2416 1.20486
PPP2CA serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Ranked 194.372 234.204 1.20493
TIPRL cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Subtracted 174.667 205.556 30.889
TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Measured 15182.5 13277.9 1904.6
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Squared Divided 468498 322755 1.45156
139 APBA1 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] Ranked 271.752 225.68 1.20415
CACNG5 voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] Rooted Subtracted 49.3267 62.4167 13.09
CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared Divided 81592.1 56211.1 1.45153
CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Measured Subtracted 12780.7 10876.4 1904.3
CHRAC1 chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Ranked 287.41 256.835 30.575
KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured Divided 2759.61 2099.49 1.31442
STAM signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] Squared Subtracted 86861.5 65369.7 21491.8
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Rooted Divided 54.9787 66.2416 1.20486
140 CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Squared 81527.6 56190.6 1.45091
FLNB filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] Rooted 55.6161 66.7332 1.19989
HLX homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774] Measured Subtracted 2597.5 698.5 1899
KCNIP2 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] Divided 2760.28 2100.27 1.31425
NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Ranked Subtracted 228.306 198.011 30.295
PRKCH protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] Squared 86609.4 65234.5 21374.9
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Ranked Divided 59 49 1.20408
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Rooted Subtracted 39.9725 52.9973 13.0248
141 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared Divided 81520.8 56188.5 1.45084
COMP cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] Ranked Subtracted 239.991 269.238 29.247
HBS1L hbs1-like. [refseq;acc:nm_006620] Measured 2597.5 698.5 1899
PRKCE protein kinase c, epsilon type (ec 2.7.1.-) (npkc-epsilon). [swissprot;acc:q02156] Squared 86600.9 65229.9 21371

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
- Hugo is the HGNC identifier if it exists
- 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/