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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measured Rank expected Gene description Hugo final
Results: HTML CSV LaTeX Showing element 1001 to 1050 of 3206 in total
measured
Rank
expected
description
Hugo
final
0.0649343 1025 0.256212 ACRC PROTEIN; PUTATIVE NUCLEAR PROTEIN. [RefSeq;Acc:NM_052957] ACRC 0.25343973
0.0649384 3150 0.993221 MELANOMA-ASSOCIATED ANTIGEN C1 (MAGE-C1 ANTIGEN) (CANCER-TESTIS ANTIGEN CT7). [SWISSPROT;Acc:O60732] MAGEC1 0.065381622
0.0649797 3141 0.993851 MELANOMA-ASSOCIATED ANTIGEN 6 (MAGE-6 ANTIGEN) (MAGE3B). [SWISSPROT;Acc:P43360] MAGEA6 0.065381732
0.0650415 3145 0.994797 MELANOMA-ASSOCIATED ANTIGEN 9 (MAGE-9 ANTIGEN). [SWISSPROT;Acc:P43362] MAGEA9 0.065381681
0.0651212 2108 0.285217 PUS7 0.228321594
0.0651239 3149 0.996058 MELANOMA-ASSOCIATED ANTIGEN 4 (MAGE-4 ANTIGEN) (MAGE-X2) (MAGE-41). [SWISSPROT;Acc:P43358] no value 0.065381634
0.0651336 2135 0.285702 HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN U (HNRNP U) (SCAFFOLD ATTACHMENT FACTOR A) (SAF-A). [SWISSPROT;Acc:Q00839] HNRNPU 0.227977403
0.0651843 852 0.250194 KINESIN-LIKE PROTEIN KIF13B (KINESIN-LIKE PROTEIN GAKIN). [SWISSPROT;Acc:Q9NQT8] no value 0.260535025
0.0652476 3144 0.997949 MELANOMA-ASSOCIATED ANTIGEN 8 (MAGE-8 ANTIGEN). [SWISSPROT;Acc:P43361] MAGEA8 0.065381698
0.0653044 2832 0.338193 CALSYNTENIN-2 PRECURSOR. [SWISSPROT;Acc:Q9H4D0] CLSTN2 0.193098024
0.0653411 1584 0.271247 HURPIN (HACAT UV-REPRESSIBLE SERPIN) (PROTEASE INHIBITOR 13) (HEADPIN) (SERPIN B13). [SWISSPROT;Acc:Q9UIV8] no value 0.240891512
0.0653467 2102 0.286165 INTS8 0.228353223
0.0653647 2103 0.286244 GON4L 0.228353083
2104 "PROTEIN KINASE C, EPSILON TYPE (EC 2.7.1.-) (NPKC-EPSILON). [SWISSPROT;Acc:Q02156]" PRKCE
0.0654179 1772 0.277203 HEAT SHOCK 70 KDA PROTEIN 1 (HSP70.1) (HSP70-1/HSP70-2). [SWISSPROT;Acc:P08107] no value 0.235992756
0.0654684 1469 0.269399 TRANSCRIPTION FACTOR RELB (I-REL). [SWISSPROT;Acc:Q01201] RELB 0.243016492
0.0654743 3152 1.00142 "MELANOMA ANTIGEN, FAMILY B, 6. [RefSeq;Acc:NM_173523]" MAGEB6B 0.065381458
3153 NECDIN. [SWISSPROT;Acc:Q99608] NDN
0.0655808 2937 0.417367 TUMOR SUSCEPTIBILITY GENE 101 PROTEIN. [SWISSPROT;Acc:Q99816] TSG101 0.157129816
0.0656049 51 0.159562 LIMKAIN B1. [RefSeq;Acc:NM_019081] KIAA0430 0.411156165
0.0656147 3184 1.32794 PYCRL 0.049410892
0.0656459 1464 0.270114 DEFORMED EPIDERMAL AUTOREGULATORY FACTOR 1 HOMOLOG (NUCLEAR DEAF-1 RELATED TRANSCRIPTIONAL REGULATOR) (NUDR) (SUPPRESSIN) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 5). [SWISSPROT;Acc:O75398] DEAF1 0.24303035
0.0657247 2761 0.324347 SAPS1 0.202636991
0.0658169 260 0.213303 NS1-ASSOCIATED PROTEIN 1. [RefSeq;Acc:NM_006372] SYNCRIP 0.308560592
0.0658246 3156 1.00678 MELANOMA-ASSOCIATED ANTIGEN 11 (MAGE-11 ANTIGEN). [SWISSPROT;Acc:P43364] MAGEA11 0.065381315
0.0659071 3154 1.00804 MAGEB18 0.065381433
0.0659913 3072 0.639469 DAB2 INTERACTING PROTEIN; NGAP-LIKE PROTEIN; DOC-2/DAB2 INTERACTIVE PROTEIN. [RefSeq;Acc:NM_032552] DAB2IP 0.103197028
0.066057 1395 0.270441 MYOSIN VIIA. [SWISSPROT;Acc:Q13402] MYO7A 0.244256603
0.0660691 1770 0.279962 HEAT SHOCK-RELATED 70 KDA PROTEIN 2 (HEAT SHOCK 70 KDA PROTEIN 2). [SWISSPROT;Acc:P54652] HSPA2 0.235993099
0.0661338 3137 1.0115 MELANOMA-ASSOCIATED ANTIGEN 10 (MAGE-10 ANTIGEN). [SWISSPROT;Acc:P43363] MAGEA10 0.065381908
0.0661546 162 0.191372 DNAJ HOMOLOG SUBFAMILY B MEMBER 11 PRECURSOR (ER-ASSOCIATED DNAJ PROTEIN 3) (ERJ3) (ER-ASSOCIATED HSP40 CO-CHAPERONE) (HDJ9) (PWP1- INTERACTING PROTEIN 4). [SWISSPROT;Acc:Q9UBS4] DNAJB11 0.345685889
0.066175 3135 1.01213 "MELANOMA ANTIGEN, FAMILY D, 4 ISOFORM 1; MAGE1 PROTEIN; MAGE-E1 PROTEIN; MAGED4 PROTEIN. [RefSeq;Acc:NM_030801]" MAGED4 0.065381917
3136 MAGEB10
0.0662042 2906 0.380173 "LYSOSOMAL ALPHA-MANNOSIDASE PRECURSOR (EC 3.2.1.24) (MANNOSIDASE, ALPHA B) (LYSOSOMAL ACID ALPHA-MANNOSIDASE) (LAMAN) (MANNOSIDASE ALPHA CLASS 2B MEMBER 1). [SWISSPROT;Acc:O00754]" MAN2B1 0.174142298
0.0662574 3134 1.01339 MELANOMA-ASSOCIATED ANTIGEN D1 (MAGE-D1 ANTIGEN) (NEUROTROPHIN RECEPTOR-INTERACTING MAGE HOMOLOG) (PRO2292). [SWISSPROT;Acc:Q9Y5V3] MAGED1 0.065381936
0.0662986 3133 1.01402 TROPHININ. [SWISSPROT;Acc:Q12816] TRO 0.065381945
0.0663724 1173 0.266132 MOTHERS AGAINST DECAPENTAPLEGIC HOMOLOG 5 (SMAD 5) (MOTHERS AGAINST DPP HOMOLOG 5) (SMAD5) (HSMAD5) (JV5-1). [SWISSPROT;Acc:Q99717] SMAD5 0.24939654
0.0666089 1210 0.26852 "BETA-2-SYNTROPHIN (59 KDA DYSTROPHIN-ASSOCIATED PROTEIN A1, BASIC COMPONENT 2) (SYNTROPHIN 3) (SNT3) (SYNTROPHIN-LIKE) (SNTL). [SWISSPROT;Acc:Q13425]" SNTB2 0.248059362
0.0666911 381 0.23892 CAPSL 0.279135694
0.066752 3151 1.02096 MELANOMA-ASSOCIATED ANTIGEN B1 (MAGE-B1 ANTIGEN) (MAGE-XP ANTIGEN) (DSS-AHC CRITICAL INTERVAL MAGE SUPERFAMILY 10) (DAM10). [SWISSPROT;Acc:P43366] MAGEB4 0.065381602
0.0669169 3140 1.02348 MELANOMA-ASSOCIATED ANTIGEN D2 (MAGE-D2 ANTIGEN) (BREAST CANCER ASSOCIATED GENE 1 PROTEIN) (BCG-1) (11B6) (HEPATOCELLULAR CARCINOMA ASSOCIATED PROTEIN JCL-1). [SWISSPROT;Acc:Q9UNF1] MAGED2 0.065381737
0.0669581 3138 1.02411 HEPATOCELLULAR CARCINOMA-ASSOCIATED PROTEIN HCA1. [RefSeq;Acc:NM_020932] no value 0.065381746
0.0670247 1001 0.262934 MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT TIM10. [SWISSPROT;Acc:Q9Y5J8] TIMM10 0.254910738
0.0670488 2339 0.303687 "6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING (EC 1.1.1.44). [SWISSPROT;Acc:P52209]" PGD 0.220782582
0.0670742 3066 0.647682 MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B (MAP1A/MAP1B LC3 B) (MAP1A/1B LIGHT CHAIN 3 B). [SWISSPROT;Acc:Q9GZQ8] MAP1LC3B 0.103560389
0.0671204 690 0.252671 RIBOSOMAL PROTEIN S6 KINASE ALPHA 6 (EC 2.7.1.37) (S6K-ALPHA 6) (90 KDA RIBOSOMAL PROTEIN S6 KINASE 6) (P90-RSK 6) (RIBOSOMAL S6 KINASE 4) (RSK-4) (PP90RSK4). [SWISSPROT;Acc:Q9UK32] RPS6KA6 0.265643465
0.0671866 688 0.25292 SIGNAL-INDUCED PROLIFERATION-ASSOCIATED 1-LIKE 1. [RefSeq;Acc:NM_015556] no value 0.265643682
0.0671887 399 0.24133 THYROID RECEPTOR INTERACTING PROTEIN 3 (TRIP-3) (FRAGMENT). [SWISSPROT;Acc:Q15649] ZNHIT3 0.278410061
0.0673124 2267 0.302153 POLYMERASE (DNA DIRECTED) SIGMA; TOPOISOMERASE-RELATED FUNCTION PROTEIN 4-1; POLYMERASE (DNA-DIRECTED) SIGMA. [RefSeq;Acc:NM_006999] POLS 0.222775878
0.0673151 398 0.241784 NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN INTERACTING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION INTERCATING PROTEIN 1; NUCLEAR FRAGILE X MENTAL RETARDATION PROTEIN-INTERACTING PROTEIN 1. [RefSeq;Acc:NM_012345] NUFIP1 0.278410068

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/