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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 313 to 362 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
79 no value Rooted serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] 63.7477 48.1588 1.3237
CACNG3 Ranked voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 254.693 202.668 1.2567
RAF1 Squared raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] 117850 70566.8 1.67005
UFC1 Measured protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 3074.57 4567.51 1.48558
80 CACNG4 Ranked voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 254.691 202.668 1.25669
PPP2R2B Rooted serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] 63.7477 48.1594 1.32368
PPP2R5E Squared serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537] 117718 70505.9 1.66962
TIA1 Measured nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 4133.47 5945.32 1.43834
81 CACNG5 Ranked voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 254.614 202.646 1.25645
CCNG2 Squared cyclin g2. [swissprot;acc:q16589] 117718 70505.9 1.66962
PPP2R2C Rooted serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] 63.7475 48.1615 1.32362
TIAL1 Measured nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 4136.36 5943.56 1.43691
82 ATF3 Rooted cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847] 60.8022 79.5099 1.30768
CCNG1 Squared cyclin g1 (cyclin g). [swissprot;acc:p51959] 117718 70505.8 1.66962
GNB5 Ranked guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] 267.636 335.359 1.25304
SNRPD1 Measured small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 4172.91 5954.48 1.42694
83 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 4932.27 7033.29 1.42597
MAGED4 Ranked melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 88.2482 110.265 1.24949
PPP2R1B Rooted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154] 63.6507 48.7127 1.30666
PPP2R5A Squared serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172] 117718 70505.9 1.66962
84 no value Measured jun dimerization protein. [refseq;acc:nm_130469] 4932.27 7033.29 1.42597
BRAF Squared b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056] 117515 70412.3 1.66896
MAGEE2 Ranked hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 88.2482 110.265 1.24949
NFYC Rooted 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] 46.7419 60.9337 1.30362
85 no value Ranked melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 88.2482 110.265 1.24949
ATG12 Squared autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 67438.6 40697 1.65709
FOSL2 Measured fos-related antigen 2. [swissprot;acc:p15408] 4941.95 7037.11 1.42395
NFYA Rooted 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] 46.7419 60.9337 1.30362
86 FOSB Measured protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539] 4942.49 7037.32 1.42384
KRAS Squared transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 105500 64146.3 1.64468
MAGEA11 Ranked melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364] 88.2482 110.265 1.24949
PPP2R1A Rooted serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] 63.6205 48.8838 1.30146
87 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] 42.2825 54.9687 1.30003
FOSL1 Measured fos-related antigen 1 (fra-1). [swissprot;acc:p15407] 4944.3 7038.04 1.42347
MAGEA2B Ranked melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356] 88.2482 110.265 1.24949
SHOC2 Squared leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 105482 64136.9 1.64464
88 no value Ranked hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 88.2482 110.265 1.24949
Squared ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211] 105482 64137.2 1.64463
KCND2 Measured potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 2411.93 1695.45 1.42259
PSEN2 Rooted presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 37.3005 48.4141 1.29795
89 CTH Measured cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 2414.22 1698.12 1.4217
HRAS Squared transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112] 105473 64132.3 1.64462
MAGEA6 Ranked melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 88.2482 110.265 1.24949
SKP1A Rooted s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] 37.3005 48.4141 1.29795
90 no value Squared transforming protein n-ras. [swissprot;acc:p01111] 105469 64130.2 1.64461
FBXW7 Rooted f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] 37.3005 48.4141 1.29795
KCND3 Measured potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] 2414.77 1698.75 1.4215
NDN Ranked necdin. [swissprot;acc:q99608] 88.2482 110.265 1.24949
91 CUL2 Rooted cullin homolog 2 (cul-2). [swissprot;acc:q13617] 37.3005 48.4141 1.29795
KCND1 Measured potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 2416.53 1700.8 1.42082

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/