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 Value Type Hugo description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 527 to 576 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
Hugo
description
red
green
network_comparison
132 Squared ATG5 autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0] 36359.2 24466.8 1.48606
Rooted HAT1 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 44.963 55.0576 1.22451
133 Measured GABARAP gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278] 23421.5 17580.4 1.33225
Ranked TOB1 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 350 290 1.2069
Squared TMEM132A gbp protein isoform a. [refseq;acc:nm_017870] 1182.25 1726.55 1.46039
Rooted OSR1 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 45.4558 55.5995 1.22316
134 Measured no value gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 21785.2 16426.1 1.32626
Ranked DAB2IP dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 350 290 1.2069
Squared GATAD2A p66 alpha. [refseq;acc:nm_017660] 81888.8 56306.5 1.45434
Rooted POLE4 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 44.849 54.7964 1.2218
135 Measured ATG3 apg3p; pc3-96 protein. [refseq;acc:nm_022488] 21785.2 16426.1 1.32626
Ranked CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 350 290 1.2069
Squared GATAD2B transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699] 81888.8 56306.5 1.45434
Rooted NCBP2 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 54.935 66.6101 1.21253
136 Measured 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] 3620.77 4763.34 1.31556
Ranked CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 350 290 1.2069
Squared no value tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735] 81888.8 56306.5 1.45434
Rooted ADIPOR2 adiponectin receptor 2. [refseq;acc:nm_024551] 41.8357 50.6469 1.21061
137 Measured 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] 3620.77 4763.34 1.31556
Ranked RASAL2 ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 350 290 1.2069
Squared CDK3 cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] 81606.8 56215.8 1.45167
Rooted MSI2 musashi 2 isoform a. [refseq;acc:nm_138962] 54.9787 66.2416 1.20486
138 Measured KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 2755.15 2094.3 1.31555
Ranked 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] 194.372 234.204 1.20493
Squared UBAC1 putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172] 468498 322755 1.45156
Rooted MSI1 musashi 1. [refseq;acc:nm_002442] 54.9787 66.2416 1.20486
139 Measured KCNIP4 potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] 2759.61 2099.49 1.31442
Ranked 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] 271.752 225.68 1.20415
Squared CCNB2 g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] 81592.1 56211.1 1.45153
Rooted ZC3H14 nuclear protein ukp68. [refseq;acc:nm_024824] 54.9787 66.2416 1.20486
140 Measured 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] 2760.28 2100.27 1.31425
Ranked RRAGA ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 59 49 1.20408
Squared CDK2 cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] 81527.6 56190.6 1.45091
Rooted 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] 55.6161 66.7332 1.19989
141 Measured SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 4405.4 5782.08 1.3125
Ranked RRAGC ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] 59 49 1.20408
Squared CCNB1 g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] 81520.8 56188.5 1.45084
Rooted REV1 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 55.6161 66.7332 1.19989
142 Measured PITRM1 metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 9276.47 7090.37 1.30832
Ranked RRAGB ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] 59 49 1.20408
Squared CDC2 cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] 81478.9 56175.2 1.45044
Rooted PRMT1 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] 55.6161 66.7332 1.19989
143 Measured ALG1 beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 9275.1 7089.65 1.30826
Ranked ANLN anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] 59 49 1.20408
Squared PPP1R13B protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] 124319 86848.2 1.43145
Rooted PRMT8 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] 55.6161 66.7332 1.19989
144 Measured UNC84A sad1/unc-84 protein-like 1. [swissprot;acc:o94901] 3349.9 4362.61 1.30231
Ranked KCNIP1 kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] 265.686 319.651 1.20312
Squared TP53BP2 tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625] 123324 86277.9 1.42938
Rooted SNRP70 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] 55.6161 66.7332 1.19989

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/