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Post by Rizwan on Nov 7, 2023 10:14:21 GMT -5
Hi,
I am working through some skeletal muscle proteomics and have noticed an issue with DAVID. I use graph-pad prism to make heatmaps using DAVID files. Some of the heat-map downloadable files on DAVID are faulty and do NOT match the actual heat-map that is displayed. As a result, the heat-maps I make using graph-pad have some columns and rows rotated, which in turn show wrong genes or pathways/functions as on or off. The original files have an error where 1 and 0 do NOT match the displayed heatmap. Is this something that can be fixed? I am happy to send example(s) if needed. Many thanks.
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Brad
DAVID Bioinformatics Team
Posts: 67
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Post by Brad on Nov 7, 2023 10:58:12 GMT -5
Hi Rizwan, If you could email an example along with your gene list, it would be very helpful. Please note that if you run an analysis and then run another for the same tool and then download the first result, you may actually get the second result as DAVID may reference the last result for download. It is always best to download the results from one analysis before moving on to another but this may not be the reason for what you have observed. Regards, Brad |
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Post by Rizwan on Nov 13, 2023 10:03:09 GMT -5
Hi Brad,
Many thanks for your response. Sorry for taking forever to get back. I had actually sent an email earlier. I will send another email now. Please let me know if you don't receive it and if you don't mind please do share the email address here.
I can confirm I always organize my analysis and results. I also had two other users run the pipeline and they had the same results.
Will email you now. Many thanks.
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Post by Rizwan on Nov 13, 2023 10:54:59 GMT -5
Hi,
I thought I will post the gene list here too should you not get my email. The issue is with cluster 7. You will notice a difference in the heatmap generated and downloadable file's raw data. Many thanks.
Protein ID Ave HZ vs WT VUL
Q8VIJ6 0.080984305
P53994 0.150800688
P35908 0.213101869
P13645 0.290196015
Q8BKC5 0.333570733
Q8VDJ3 0.368853137
Q7TSH2 0.397641495
Q99PL5 0.413964024
P19324 0.42571954
P06728 0.431903563
Q8BMK4 0.435820892
P18826 0.440156623
Q91W90 0.448150936
Q8CIE6 0.454323974
P01027 0.454763201
Q99KK7 0.462812351
Q3UPL0 0.469975376
Q6ZQ73 0.470544905
Q9EQK5 0.492180876
Q4VAA2 0.507709013
Q99MN1 0.508701754
Q61584 0.512067247
P62821 0.515321749
Q9CYT6 0.527285122
P11276 0.528858855
O35295 0.532374683
B1AR69 0.53720265
P99024 0.538705365
Q99MS7 0.543785081
Q9JIF7 0.561527915
Q99MR9 0.563411735
P70670 0.569506993
Q99ME6 0.581866533
P04264 0.582559565
F6TQW2 0.58543781
P62737 0.596930116
Q922J3 0.599393082
P60867 0.601390313
P27546 0.604781788
Q9WTR5 0.60600347
Q9JMH9 0.607866845
P31230 0.616506934
P42932 0.619558024
P49813 0.632506927
Q8BWY3 0.632666597
P51150 0.637175742
Q91X72 0.637622235
P61255 0.63835628
Q8BGD9 0.640464545
O08547 0.643521641
P19253 0.644272053
P62908 0.644735309
P14211 0.645352244
P47811 0.645957549
P41105 0.649119341
P70236 0.651760095
Q3V1D3 0.652429019
P62751 0.654071604
P14148 0.654692987
P80313 0.656710613
Q8R4S0 0.662702881
Q61838 0.66323633
P62274 0.665291065
P29699 0.66584394
P08551 0.667516451
P62911 0.668908543
Q9R062 0.669887833
Q9D8E6 0.673124123
O70400 0.676675915
P61027 0.677135183
Q922R8 0.678016474
Q80XB4 0.678387464
Q9D0I9 0.682616826
P58281 0.686655399
E9Q3H6 0.686851451
P27773 0.691623172
P14115 0.695842572
P62267 0.697056083
P57780 0.701187593
Q8C7E7 0.703946894
P53026 0.704915812
Q8R1B4 0.70738364
P07309 0.709623706
P83882 0.709797937
P08113 0.711020486
Q8CGC7 0.714242366
P62242 0.71429043
Q9Z0N1 0.715470359
Q61398 0.716902274
Q9QZD9 0.717798366
Q5DTJ9 0.718096451
Q5XJY5 0.719614315
P47963 0.719989842
E9PWZ3 0.72124484
Q9CZ04 0.72322818
Q04447 0.723276381
P80318 0.724325607
Q9CZM2 0.724532577
O09110 0.725213669
P62702 0.725839083
P08003 0.727418752
P47911 0.729321798
P80314 0.730742042
Q9DCD0 0.733560369
O35887 0.73490295
Q61595 0.735079991
E9PV24 0.735207918
O08788 0.735556277
Q9WV35 0.735605291
Q78PY7 0.73625566
Q9WUB3 0.736609337
P11499 0.737444612
P62245 0.738642239
P14869 0.74297888
Q9CRB6 0.743529514
P61358 0.744086973
Q9Z1Z0 0.746135934
P14131 0.748755177
Q6PHQ9 0.749030664
Q8BWB1 0.749884276
P80316 0.750489255
P62754 0.751813858
P47915 0.75196795
Q9DB60 0.752534956
P62281 0.752546932
P35527 0.757127971
Q921I1 0.75787728
Q3B7Z2 0.761706759
P49312 0.762891042
O88545 0.764560505
P57776 0.76703706
Q8BP67 0.768184353
P08226 0.77161728
Q6ZWN5 0.774058335
Q9CR57 0.775896987
P63323 0.776723598
Q9CZX8 0.778281711
P62918 0.778685918
Q6NZJ6 0.783969505
P18654 0.784969109
Q8BMS4 0.785465979
P26638 0.786824386
Q6ZWY3 0.789809134
Q9D0J8 0.790092615
O08529 0.791273791
Q6ZWV3 0.792588336
P84099 0.792927141
O35350 0.793567015
Q9QZF2 0.795363651
P35979 0.796376415
Q9DCL9 0.796409787
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Post by Rizwan on Nov 13, 2023 10:56:02 GMT -5
And just the list here:
Q8VIJ6
P53994
P35908
P13645
Q8BKC5
Q8VDJ3
Q7TSH2
Q99PL5
P19324
P06728
Q8BMK4
P18826
Q91W90
Q8CIE6
P01027
Q99KK7
Q3UPL0
Q6ZQ73
Q9EQK5
Q4VAA2
Q99MN1
Q61584
P62821
Q9CYT6
P11276
O35295
B1AR69
P99024
Q99MS7
Q9JIF7
Q99MR9
P70670
Q99ME6
P04264
F6TQW2
P62737
Q922J3
P60867
P27546
Q9WTR5
Q9JMH9
P31230
P42932
P49813
Q8BWY3
P51150
Q91X72
P61255
Q8BGD9
O08547
P19253
P62908
P14211
P47811
P41105
P70236
Q3V1D3
P62751
P14148
P80313
Q8R4S0
Q61838
P62274
P29699
P08551
P62911
Q9R062
Q9D8E6
O70400
P61027
Q922R8
Q80XB4
Q9D0I9
P58281
E9Q3H6
P27773
P14115
P62267
P57780
Q8C7E7
P53026
Q8R1B4
P07309
P83882
P08113
Q8CGC7
P62242
Q9Z0N1
Q61398
Q9QZD9
Q5DTJ9
Q5XJY5
P47963
E9PWZ3
Q9CZ04
Q04447
P80318
Q9CZM2
O09110
P62702
P08003
P47911
P80314
Q9DCD0
O35887
Q61595
E9PV24
O08788
Q9WV35
Q78PY7
Q9WUB3
P11499
P62245
P14869
Q9CRB6
P61358
Q9Z1Z0
P14131
Q6PHQ9
Q8BWB1
P80316
P62754
P47915
Q9DB60
P62281
P35527
Q921I1
Q3B7Z2
P49312
O88545
P57776
Q8BP67
P08226
Q6ZWN5
Q9CR57
P63323
Q9CZX8
P62918
Q6NZJ6
P18654
Q8BMS4
P26638
Q6ZWY3
Q9D0J8
O08529
Q6ZWV3
P84099
O35350
Q9QZF2
P35979
Q9DCL9
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