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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Gene Hugo Rank description measured expected final
Results: HTML CSV LaTeX Showing element 2708 to 2757 of 3206 in total
Hugo
Rank
description
measured
expected
final
SLC27A6 2711 VERY LONG-CHAIN ACYL-COA SYNTHETASE HOMOLOG 1. [RefSeq;Acc:NM_014031] 0.46044 2.22067 0.207342829
SLC2A6 1244 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 6 (GLUCOSE TRANSPORTER TYPE 6) (GLUCOSE TRANSPORTER TYPE 9). [SWISSPROT;Acc:Q9UGQ3]" 0.0527752 0.213145 0.247602336
SLC2A8 1245 "SOLUTE CARRIER FAMILY 2, FACILITATED GLUCOSE TRANSPORTER, MEMBER 8 (GLUCOSE TRANSPORTER TYPE 8) (GLUCOSE TRANSPORTER TYPE X1). [SWISSPROT;Acc:Q9NY64]" 0.069385 0.280228 0.247601953
SLC30A9 2945 0.103715 0.679961 0.152530807
SLC35B1 1923 "SOLUTE CARRIER FAMILY 35, MEMBER B1; UDP-GALACTOSE TRANSPORTER RELATED. [RefSeq;Acc:NM_005827]" 0.0974156 0.419969 0.231959026
SLC35D2 667 SQV-7-LIKE PROTEIN (FRAGMENT). [SPTREMBL;Acc:O95454] 0.104453 0.391317 0.266926814
SLC37A1 913 GLYCEROL-3-PHOSPHATE TRANSPORTER (G-3-P TRANSPORTER) (G-3-P PERMEASE). [SWISSPROT;Acc:P57057] 0.0275088 0.106609 0.2580345
SLC37A2 912 0.0349547 0.135465 0.258034917
SLC39A6 1733 "LIV-1 PROTEIN, ESTROGEN REGULATED. [RefSeq;Acc:NM_012319]" 0.0166846 0.0703876 0.23703891
SLC39A7 1427 HISTIDINE-RICH MEMBRANE PROTEIN KE4. [SWISSPROT;Acc:Q92504] 0.109553 0.449228 0.243869483
SLC3A1 1812 "NEUTRAL AND BASIC AMINO ACID TRANSPORT PROTEIN RBAT (B(0,+)-TYPE AMINO ACID TRANSPORT PROTEIN) (NBAT) (D2H). [SWISSPROT;Acc:Q07837]" 0.0214423 0.0914656 0.234430212
SLC45A2 1289 MEMBRANE-ASSOCIATED TRANSPORTER PROTEIN (AIM-1 PROTEIN) (MELANOMA ANTIGEN AIM1). [SWISSPROT;Acc:Q9UMX9] 0.0493513 0.200615 0.24600005
SLC46A1 837 0.152414 0.584621 0.260705654
SLC46A2 846 THYMIC STROMAL CO-TRANSPORTER. [RefSeq;Acc:NM_033051] 0.106987 0.410377 0.260704182
SLC46A3 838 0.152414 0.584621 0.260705654
SLC47A1 2209 0.128228 0.569623 0.225110292
SLC47A2 2207 0.098654 0.437657 0.225413966
SLC4A1AP 2876 "SOLUTE CARRIER FAMILY 4 (ANION EXCHANGER), MEMBER 1, ADAPTOR PROTEIN; KIDNEY ANION EXCHANGER ADAPTOR PROTEIN; KANADAPTIN; LUNG CANCER ONCOGENE 3. [RefSeq;Acc:NM_018158]" 0.0374428 0.198705 0.188434111
SLC5A5 2575 SODIUM/IODIDE COTRANSPORTER (NA(+)/I(-) COTRANSPORTER) (SODIUM-IODIDE SYMPORTER) (NA+/I-SYMPORTER). [SWISSPROT;Acc:Q92911] 0.30514 1.43033 0.213335384
SLC5A6 2571 SODIUM-DEPENDENT MULTIVITAMIN TRANSPORTER (NA(+)-DEPENDENT MULTIVITAMIN TRANSPORTER). [SWISSPROT;Acc:Q9Y289] 0.248255 1.16362 0.213347141
SLC5A8 2572 "SOLUTE CARRIER FAMILY 5 (IODIDE TRANSPORTER), MEMBER 8; APICAL IODIDE TRANSPORTER. [RefSeq;Acc:NM_145913]" 0.257307 1.20606 0.213345107
SLIT1 2350 0.0498274 0.22609 0.220387456
SLMO1 749 ERYTHROID DIFFERENTIATION AND DENUCLEATION FACTOR 1. [SWISSPROT;Acc:O60584] 0.0317812 0.120157 0.264497283
SLMO2 740 PROTEIN C20ORF45 (CGI-107). [SWISSPROT;Acc:Q9Y3B1] 0.0385694 0.145821 0.264498255
SLU7 657 STEP II SPLICING FACTOR SLU7. [RefSeq;Acc:NM_006425] 0.0404532 0.151367 0.267252439
SMAD1 1175 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 1 (SMAD 1) (MOTHERS AGAINST DPP HOMOLOG 1) (MAD-RELATED PROTEIN 1) (TRANSFORMING GROWTH FACTOR- BETA SIGNALING PROTEIN-1) (BSP-1) (HSMAD1) (JV4-1). [SWISSPROT;Acc:Q15797] 0.0726422 0.291272 0.24939644
SMAD2 1168 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 2 (SMAD 2) (MOTHERS AGAINST DPP HOMOLOG 2) (MAD-RELATED PROTEIN 2) (HMAD-2) (JV18-1) (HSMAD2). [SWISSPROT;Acc:Q15796] 0.0322934 0.129486 0.249396846
SMAD3 1169 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 3 (SMAD 3) (MOTHERS AGAINST DPP HOMOLOG 3) (MAD3) (HMAD-3) (MMAD3) (JV15-2) (HSMAD3). [SWISSPROT;Acc:Q92940] 0.0326423 0.130885 0.249396799
SMAD4 927 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 4 (SMAD 4) (MOTHERS AGAINST DPP HOMOLOG 4) (DELETION TARGET IN PANCREATIC CARCINOMA 4) (HSMAD4). [SWISSPROT;Acc:Q13485] 0.303187 1.17661 0.257678415
SMAD5 1173 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5 (SMAD 5) (MOTHERS AGAINST DPP HOMOLOG 5) (SMAD5) (HSMAD5) (JV5-1). [SWISSPROT;Acc:Q99717] 0.0663724 0.266132 0.24939654
SMAD9 1171 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 9 (SMAD 9) (MOTHERS AGAINST DPP HOMOLOG 9) (SMAD9) (MADH6). [SWISSPROT;Acc:O15198] 0.0614057 0.246217 0.24939667
SMARCA1 1236 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L1. [SWISSPROT;Acc:P28370] 0.271278 1.09519 0.247699486
SMARCA2 1234 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L2 (SNF2-ALPHA). [SWISSPROT;Acc:P51531] 0.130458 0.526678 0.247699733
SMARCA4 1235 POSSIBLE GLOBAL TRANSCRIPTION ACTIVATOR SNF2L4 (SNF2-BETA) (BRG-1 PROTEIN) (MITOTIC GROWTH AND TRANSCRIPTION ACTIVATOR) (BRAHMA PROTEIN HOMOLOG 1). [SWISSPROT;Acc:P51532]
SMARCA5 1237 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN A5; SUCROSE NONFERMENTING-LIKE 5. [RefSeq;Acc:NM_003601] 0.307072 1.2397 0.247698637
SMARCB1 1141 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY B MEMBER 1 (INTEGRASE INTERACTOR 1 PROTEIN) (HSNF5) (BAF47). [SWISSPROT;Acc:Q12824]" 0.108251 0.43247 0.250308692
SMARCC1 1227 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN C1; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 155; SWI/SNF COMPLEX 155 KDA SUBUNIT; CHROMATIN REMODELING COMPLEX BAF155 SUBUNIT. [RefSeq;Acc:NM_003074] 0.720529 2.90646 0.247906044
SMARCC2 1248 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN C2 ISOFORM A; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 170; CHROMATIN REMODELING COMPLEX BAF170 SUBUNIT; SWI3-LIKE PROTEIN; SWI/SNF COMPLEX 170 KDA SUBUNIT. [Sou 0.66815 2.69939 0.247518884
SMARCD1 388 "SWI/SNF RELATED, MATRIX ASSOCIATED, ACTIN DEPENDENT REGULATOR OF CHROMATIN SUBFAMILY D MEMBER 1 (SWI/SNF COMPLEX 60 KDA SUBUNIT) (BRG1- ASSOCIATED FACTOR 60A). [SWISSPROT;Acc:Q96GM5]" 0.140567 0.504282 0.278746812
SMARCD2 389 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D2; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60B; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60B SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT B. [Sour 0.0474703 0.170299 0.278746792
SMARCD3 390 SWI/SNF-RELATED MATRIX-ASSOCIATED ACTIN-DEPENDENT REGULATOR OF CHROMATIN D3; RSC6P; MAMMALIAN CHROMATIN REMODELING COMPLEX BRG1-ASSOCIATED FACTOR 60C; SWP73-LIKE PROTEIN; CHROMATIN REMODELING COMPLEX BAF60C SUBUNIT; SWI/SNF COMPLEX 60 KDA SUBUNIT C. [Sour 0.123465 0.44293 0.278746077
SMOC2 660 SECRETED MODULAR CALCIUM-BINDING PROTEIN 2; SMOOTH MUSCLE ASSOCIATED PROTEIN 2. [RefSeq;Acc:NM_022138] 0.035822 0.134108 0.267113073
SMOX 442 POLYAMINE OXIDASE ISOFORM 1; POLYAMINE OXIDASE; FLAVIN-CONTAINING SPERMINE OXIDASE; PUTATIVE CYCLIN G1 INTERACTING PROTEIN; FLAVIN CONTAINING AMINE OXIDASE. [RefSeq;Acc:NM_019025] 0.0602832 0.217862 0.276703601
SMPD2 2849 SPHINGOMYELIN PHOSPHODIESTERASE 2 (EC 3.1.4.12) (NEUTRAL SPHINGOMYELINASE) (NSMASE) (N-SMASE) (LYSO-PLATELET ACTIVATING FACTOR- PHOSPHOLIPASE C) (LYSO-PAF-PLC). [SWISSPROT;Acc:O60906] 0.696087 3.6375 0.191364124
SNAI2 735 ZINC FINGER PROTEIN SLUG (NEURAL CREST TRANSCRIPTION FACTOR SLUG) (SNAIL HOMOLOG 2). [SWISSPROT;Acc:O43623] 0.0869475 0.328537 0.264650557
SNAP29 799 SYNAPTOSOMAL-ASSOCIATED PROTEIN 29 (SNAP-29) (VESICLE-MEMBRANE FUSION PROTEIN SNAP-29) (SOLUBLE 29 KDA NSF ATTACHMENT PROTEIN). [SWISSPROT;Acc:O95721] 0.14026 0.535319 0.262011997
SNAP91 416 CLATHRIN COAT ASSEMBLY PROTEIN AP180 (CLATHRIN COAT ASSOCIATED PROTEIN AP180) (91 KDA SYNAPTOSOMAL-ASSOCIATED PROTEIN). [SWISSPROT;Acc:O60641] 0.212723 0.766919 0.277373491
SNAPAP 1274 SNARE ASSOCIATED PROTEIN SNAPIN. [RefSeq;Acc:NM_012437] 0.0384625 0.155989 0.246571874
SNF8 1734 EAP30 SUBUNIT OF ELL COMPLEX. [RefSeq;Acc:NM_007241] 0.04274 0.180308 0.237038845
SNORA7A 1927 60S RIBOSOMAL PROTEIN L32. [SWISSPROT;Acc:P02433] 0.716691 3.09201 0.23178806

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/