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 544 to 593 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
136 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 3620.77 4763.34 1.31556
137 CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Squared 81606.8 56215.8 1.45167
MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] Rooted 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
138 KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Measured 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
UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] Squared 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
CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Squared 81592.1 56211.1 1.45153
KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Measured 2759.61 2099.49 1.31442
ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] Rooted 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
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] Measured 2760.28 2100.27 1.31425
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Ranked 59 49 1.20408
141 CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Squared 81520.8 56188.5 1.45084
REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Rooted 55.6161 66.7332 1.19989
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Ranked 59 49 1.20408
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Measured 4405.4 5782.08 1.3125
142 CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Squared 81478.9 56175.2 1.45044
PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] Measured 9276.47 7090.37 1.30832
PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Rooted 55.6161 66.7332 1.19989
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Ranked 59 49 1.20408
143 ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] Measured 9275.1 7089.65 1.30826
ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] Ranked 59 49 1.20408
PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Squared 124319 86848.2 1.43145
PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Rooted 55.6161 66.7332 1.19989
144 KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] Ranked 265.686 319.651 1.20312
SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Rooted 55.6161 66.7332 1.19989
TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] Squared 123324 86277.9 1.42938
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Measured 3349.9 4362.61 1.30231
145 no value filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Rooted 55.6161 66.7332 1.19989
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Squared 310840 442993 1.42515
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Measured 16771.5 12889.1 1.30122
KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] Ranked 265.639 319.546 1.20293
146 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] 265.632 319.531 1.20291
PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Rooted 55.0737 66.0298 1.19894
RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Squared 103496 146848 1.41888
STAMBPL1 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Measured 11068 8508.5 1.30082
147 no value nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] Ranked 50.7983 42.3003 1.2009
CHMP2A putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] Measured 11068 8508.5 1.30082
FOXP4 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Rooted 42.0574 50.4237 1.19893
RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Squared 103496 146848 1.41888
148 FOXP1 forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Rooted 42.0577 50.424 1.19892
RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Squared 103496 146848 1.41888
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Measured 11068 8508.5 1.30082
UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] Ranked 296.677 247.559 1.19841
149 no value atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 142 170 1.19718

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/